The main problem I have with the ending of the Shepard trilogy, and I'm calling it the Shepard trilogy is because they've said it isn't the end of Mass Effect, but the end of Shepard's story arc, although I can already see a point where they left themselves an out, but that's another thread.
Back to my original sentence... The main problem I have with the ending is that it doesn't fit with the pace of the story. The subject matter "we bring order to the chaos" was brought up in ME1 by Sovereign. Fine. "We are your salvation through your destruction." in ME2. Fine. And now the war.
Yes, the war. This war has been going on between reapers and organics for a billion years, at least. But even the reapers started small. They didn't start with enough ships to blacken the sky of every world. Some race who probably built the entire system of Mass Relays (including a big one in darkspace), Citadel, Starbrat was so full of self-loathing they had themselves and every other race in the galaxy harvested by their creations, the reapers, and put them on a timer to do this. So there were probably about 15 in the beginning. They called it ascension.
The whole premise that they can't be stopped is just mind boggling, and given what they do to worlds after they harvest them, there simply are not enough worlds in the galaxy capable of supporting life for them to have been able to do this for so long at regular 50,000 yr intervals. They've always used the same strategy. So this means 1) there aren't as many of them as we think there are; 2) this time it's different.
The plot is cheesy and filled with one-liners. It's not your "pure RPG". It's a sci-fi action-RPG-shooter featuring our favorite action hero, Commander Shepard, who has more one-liner renegade interrupts per 2 hrs of game than Arnold Schwarzenegger did in his 1980s action movies, and the one liners are just as cheesy, and we love them. Of course the pure paragon players don't see this side of the game. Their loss.
I play Shepard in her glorious badassery. And does Shepard wear her N7 armor in the game? No. Why? She's the action hero. Action heroes wear something over the top, like Blood Dragon Armor. Action heroes try ryncol. Action heroes throw bad guys out windows on the 30th floor. Action heroes swear when their big assed gun (Cain) doesn't work (glitch) and then take out the boss (human proto-reaper) with a Carnifex and biotics.
Action heroes do stupid things, like fly a fighter up into the bottom of the Citadel and land it in the council chamber and open the arms. Oh wait, that would have actually been logical... No the stupid thing was running across a glassed crater of no-man's land guarded by a capital ship (where someone has been kind enough to plant some ornamental shrubbery), where water was flowing uphill, and this capital ship was firing at everyone charging at the beam. -- you know the beam. The one the reapers were tossing humans into to be made into goop? That one. Then a laser from the ship probably set to "stun" NEARLY hit our action hero -- reapers don't want to kill Shepard. They WANT Shepard.
(For the reapers wanting Shepard I refer you to all the Harbinger conversations in ME2: "Surrender and you will be spared." "If I must destroy you, Shepard, I will." "We are your destiny." They wanted Shepard alive. Shepard was needed because Shepard wasn't indoctrinated.)
Then things go wonky. Suddenly that Eviscerator she was carrying is gone and a pistol is in her hand. And someone explain how she managed to change clothes? Or rather, WHO changed her clothes? No longer in that Blood Dragon Armor I'd paid 50,000 CR, but in charred N7 armor. And where did that "Shepard you're bleeding." "I don't have time to bleed" attitude go?
This is where everything stopped making sense. This is where the writers passed "Go" on the way to the funny farm. Why was Saren, for example, able to shoot the keepers in ME1, but Shepard unable to do so with that pistol? No I'm not going by Indoctrination Theory. I'm going by the "Lack of Peer Review Theory".

So we get to the Anderson/TIM scene where TIM is playing puppetmaster, followed by shooting TIM via interrupt -- Shepard still has a little bit of spunk left. Then Anderson dies which was a cliche scene that always works. But then we get the elevator to WTFland which I assume is the level of the crucible right above where Anderson bought the farm.
And here's another place where I have a major problem with the ending. It simply didn't make any sense. Starbrat explains its twisted and faulty logic, Shepard makes a lame attempt at challenging, and Starbrat shoots it down. Apparently challenging anything isn't going to work because no matter what Starbrat is 100% correct because Starbrat is flawless. <_< I wanted to pick it up and throw it over the side in an "Hasta la vista, baby." moment. But alas, Shepard was now Mac's Shepard, not mine. So Starbrat tells me that my being there means that its solutions won't work anymore and it came up with three new solutions, and tells me that I have choice, more than I know. Wow!!!
1) Control - I die. I lose everything I have. The reapers will obey me. The mass relays will be destroyed. 2) Destroy - I can destroy all synthetic life (including the Geth), and the reapers, and Starbrat. Even I am part synthetic - but what does this mean? But tells me that my children will eventually create synthetics and the cycle will start again. The mass relays will be destroyed. 3) Synthesis - I die. I rewrite the genetic code of every living creature in the galaxy to be part synthetic and part organic. I do this without their permission. The cycles end. The mass relays will be destroyed. Wow. This is some choice. I destroy galactic civilization in all endings. I am guaranteed death in two of them. Starbrat and the reapers survive in two of them. So this tells me that only one ending is even remotely good -- Destroy. Synthesis means people will never look at their toaster the same. I don't see the point of control other than an Ayn Rand power trip. Two of them mean you've given up hope. But they are all bad. All of them are bad. Sophie's Choice Dilemma.
This is an open ending? No. This is the ending where Mac and Casey decide "We're taking our toys and going home ending." There is simply no good choice in this ending. They are all bad. Where is this choice? Shepard lights a cigar.
"Look you little ****er. (blows smoke in Starbrat's face) I'm not playing your game anymore. Joker, you copy?"
"Yes, Commander."
"Send in a shuttle for pickup and plan 'B'."
"Roger that, Commander."
Starbrat asks, "What's plan 'B'"
"A big surprise."

-- 50 MT antimatter nuke. Bye bye Citadel, Starbrat, AI of reaper brain.