sorry for the long post.
I'm new to the forum,
but after playing thru ME3 (orig and ex-cut) several times and letting it digest, I've come to a few conclusions about why I have complaints and issues, beyond the fact that BioWare is killing the ME series. For starters, I love ME2! But, parts of ME3 were very good as well, but overall, it was found wanting.
The battle scenes, sound effects, soundtrack and graphics were phenomenal, beautiful and performed flawlessly for me. But, as has been addressed, it became a shooter, which, for the ME universe, is a fail, albeit, if they would've switched back to the RPG after the battles it would have been fine, the ME series always reminded me of a highly interactive movie, and I liked that. I liked seeing all my decisions and choices played out through the game.
Furthermore, there were several occasions where, I found myself choked up (as I did in ME2) (now, I'm not a wuss, by a long shot, but having to say goodbye to a respected superior, or saying last possible goodbyes to old friends and fellow squad mates, is always hard.) So parts of the storyline were good.
One of my complaints, that, some of y'all have touched on, were the undeveloped speech options. Specifically, the options related to "how Shep felt" after certain traumatic events, loads of stress and neg occurrences. I always choose those speech options, but they dead-ended with some lame comment, such as; "you'll be okay Shepard" or "you can't save them all Shepard". I would have liked to have seen that developed more, to show that, Shep wasn't superhuman, cold or unfeeling. Fact is, when individuals experience traumatic events, at some point they have to let it out or discuss it, or it will tear them up from inside out with the typical neg consequences. I was really wanting a momentary "Shep break down" scene. Where he;
goes into the med bay, wearing his armor, minus helmet, to have the doc check a shoulder wound. But instead he tells the doc, "I...can't sleep.." and when the doc tries to hand him sleep agents, Shep responds "no...every time I close my eyes....I see the child...I watched die..." never making eye contact with the doc. Of course, the doc would've made that lame "you can't save em all Shepard" response. To which, I wanted Shep to explode, maybe, rip a surgical table out of the floor and throw it across the med bay (away from doc, of course) then, he breaks down further, and into a rant along the lines of "if i sacrifice the innocent what have i gained...more importantly.....what have I lost?!?" "people are looking to me to solve everything...to have all the answers...they're throwing their lives away, in my name!....Why me?!? I'm just a soldier! My life doesn't have more value than anyone else's life!!! In fact...my life is probably worth less....Cerebrus has the catalyst...I failed" Shep punches a med bay wall (leaving a large dent) At which point Shep collapses on the floor with his back against a med bay wall, staring off into space, with tears rolling down his face (but not crying) cutting into the battle field dirt and grime on his face. The doc immediately calls Sheps friends and romanced character, (Garrus, Kaiden, Tali etc in my games) they pick Shep up, escort him to his cabin (providing cover), where Garrus and Kaiden stand guard outside Shep's cabin and say something along the lines of "no one gets into Shepard's cabin! Roger that!" as Tali, locks the door, removes his armor, tends to his wound, maybe cleans his face. The entire time Tali has her helmet off,( in front of Shep only, of course) Tali speaks to him softly, something along the lines of "I will keep the nightmares away my love" and "when this is over, my love, you still owe me a house on the home-world. We've both given so much of ourselves to fighting and political work, it's time we become selfish with each other". Tali puts Shep to bed and they both fall asleep, Tali is awakened by Shep's nightmare and she wakes him, saying "I've got you" but the next time she wakes, Shep is gone, she panics briefly but she finds him at the fish tank, where, he makes an analogy about the fish and if, they viewed humans killing them, as we view reapers and what chance do they...we... have?!? Etc etc. Tali asks about the nightmares and puts him back to bed, speaking to him softly, as Tali starts to slip into sleep, she hears Shep, finally, say, "Tali...I....love you" she smiles and says "I know my love" as she holds him tighter than ever. When Shep and Tali get up, they get dressed, but Tali doesn't leave Shep's side, realising, how far Shep has let her in. Garrus and Kaiden each come in the room and talk to Shep. Something along the lines of; "You've always been there for us and you've never lead us wrong or let us down. We're here whenever you need us, for anything, Old Friend" (AKA they put him back together again) Naturally, the doc pays him a visit, and Shep trys to apologize, but the doc cuts him off and says something along the lines of "my dear commander Shepard, you have nothing to apologize for, I'm glad to see you're still human...but, next time, my dear commander.......talk to me sooner, the med bay equipment would last longer. And, I'd recommend another 6-8hrs of rest...but, I doubt you'll take my advice.....perhaps, Tali can assist me with my recommendation"...doc winks at Tali, and asks to speak to her outside. As they speak, doc says "he's hurting Tali, and honestly, I think you can help him more than I" as she turns to walk away, she turns back..."by the way....it's a rare thing to see the commander in love...I approve....it looks good, on both of you...even if I am a bit jealous, my dear." in her heavy English accent.
This would have been an easy and simple way to show Shep's humanity and furthermore that Shep is not a cold, unfeeling automaton and brought the game firmly back into the RPG realm. It also, I feel, would've made a better connection between gamer and character. After all, those of us that have been in....hostile or devastating situations would sympathise with and understand this reaction completely.
My other issue was, Shep's lack of injuries, meaning, he can fall 60ft, bounce, then get right up and start shooting. Or he, gets blasted 70ft into a wall, hops up and starts shooting. How? If the gamer can kill him....he should become injured from time to time. I would've liked to see, Shep's team having to pull his unconscious or injured body back to the ship, just to show A) he can be injured and he is not super human.

his crew's loyalty.
Most everyone has been hospitalised for various reasons, some more serious than others. And the one thing you learn is; who your friends are and who actually cares. It also forces you to except your limits. It tends to re-focus most of us, remind us, what's worth fighting for and what's truly important in our lives.
I completely agree with all your comments about the crucible and the catalyst. Talk about, out of left field! Considering all the high tech hackers in the ME universe, (besides, Kasumi, Solarians, Asari, Quarians, Geth etc etc) there'd be no way a Protheian device of that magnitude could have stayed hidden, that long, directly under everyone's nose! Its all way to...convenient. It would have been way more believable, if it was on an undiscovered, unknown or unexplored planet.
I'm also confused by the lack of attempts on Shep's life. Cerebrus and the Reapers know he's "getting in the way". At some point, one or both would've made an attempt or two, to "remove the problem" but no...Some would say that Cerebrus attempted it at their base. But Shep was being a thorn in their side long before that. So the "attempt" was...weak, at best. It would have been surprising, to say the least, to most, if an attempt on Shep's life was made, on the Normandy. Talk about a thriller.
That brings us to the endings. The orig ending left and created alot of questions. The ex-cut ending still left and created questions, but it did answer some- so, it was better. Here are my issues; why did the Normandy crew leave Shep? They have no prob disobeying orders, and Shep didn't leave Joker on the SR1! But they just left?!? Why?
And Garrus was the one that said "they had to leave"?!? Talk about a complete betrayal by the Normandy crew.....ask any firefighter, LEO or soldier-you NEVER leave a man, a friend behind! Particulary, one that saved your ass on multiple occasions, and gave his life for you before. Joker would have said "F$!? The orders! We're getting Shepard! Same for everyone else!
Now, someone correct me if I'm wrong, but the planet the Normandy (SR2) went down on, is the same planet the ole man and kid were talking, (after the credits) correct? That brings up more questions! Like, who stayed? Why? Did the Normandy ever leave? Etc etc
Now discussing the ending related to Shep. I created several endings in my head as i played through ME3, that would've brought closure and a better, all around ending. For example, Shep has always fostered relationships with people he didn't know. He never asked, "what do I get out of it" he just selflessly put his life on the line for people, that later became friends. So, one ending I thought of, would have brought those relationships full circle; Shep detonates the catalyst- as it starts to explode, he collapses, suddenly a biotic bubble surrounds him, Kasumi appears next to him in the protective bubble, "we got you Shep!" Samara, yells "my field can't protect them from the explosion!" another biotic barrier appears between the explosion and the bubble, with Shep and Kasumi, Jack yells "I got it!" Jacob runs in to help pull Shep out. (I'm using my character choices as examples)
Now there's 2 options to complete this ending A) Shep dies, surrounded by his friends. Or

his friends pull Shep's ass out of the fire (literally) for the first time and its left open.
Ideally, it should be the Normandy crew saving him, just on pure principal. A nice ending would have been Garrus, Kaiden etc (whomever your game save imported) drag Shep towards the Normandy, when a few husks appear and are immediately blasted by a shot gun, that Tali is holding and she says something along the lines of "stay away from my man, bosh'tets!!!!" (this scenario would play out with whomever your Shep romanced)
A surprising ending would have been; as Shep detonates the catalyst, he collapses, but just before losing consciousness, he sees a form coming towards him. The cutscene reveals Kolyat, pulling Shep out and into a shuttle. Kolyat notifies the Normandy of his pick up, but notes; "The Commander is in very bad shape.."
Another nice ending, would have been a zoom in of a house, on the Quarian home world. As you get closer, you see Shep bandaged up, next to Tali with no mask. Then a pan out. Fitting...
But the endings available in the game now are- he suffers and dies alone or he suffers alone but seems to live. Completely negating all the friendships he fostered! Where were they when HE needed THEM?!?! Which brings up questions as well.
The side missions are very disappointing-fly to planet, scan, go back....why even bother?
The weapon customisations, seemed great, at first, but then I realised you only ever get 2 slots. I had hoped as you progressed through the game, you would unlock/earn more slots..but, no.
So I'm 50/50 on ME3, orig and ex-cut, I'm disappointed in the endings, I expected more, to say the least. And I definitely expected a better level boss at the end. But I also expected a better solution to the Reapers.
I can only hope, that BioWare, continues to produce Mass Effect games and not just DLC. I read a quote by someone, but can't recall, who or where I read it, so i cant give credit, but it went something like; " With BioWare ending the Mass Effect series, I can see BioWare sliding into obscurity."
That's a very real possibility, they have a huge following with ME, it'd be foolish to throw away guaranteed, revenue producing games that already have a following, the backlash from fans prove the following of the ME series. It'd be like testing a new pistol....on your foot!