Each game has its strengths and weaknesses. The following is not an objective review as there is no such thing, but is completely my opinion.
Story: I have to give this one to ME1. Clear goals, consistant plot and a great ending, but a bit weak when it comes to fleshing out the characters. Wrex, Garrus and Liara are the only ones with personal missions.
(warning ME1 spoilers which should be fine here as the forum rules say no ME3 spoilers.) Wrex with Virmire and the Genophage cure. This is a real turning point for the character, when he goes from being just a Merc to a leader of his people. Or you could just killl him.
Garrus with Dr. Saleon. This is a moment where he goes from being a CSec officer to a vigilante. Or you can just skip this entirely.
Liara and her mother Matriarch Benezia on Noveria. There is some great dialog between the two and gives great insight into Liara's background. Or you could just not bring Liara along on the mission.
The real problem is that there are no corresponding missions for Tali, Kaidan or Ashley. You do get a great mission for Tali in ME2, but why so little love for Kaidan/Ashley? They're with you the longest in ME1 but are almost completely absent from ME2 and only really join you toward the end of ME3.
When it comes to story, ME2 and ME3 don't compare favorably. ME2 has plot problems right from the beginning with space Jesus. I really hated that idea. For a more indepth analysis check out smudboy's youtube review of ME2.
www.youtube.com/watch I will give ME2 one thing and that is character devolopment.
As for ME3 the quality of the story is inconsistant. Some of the stories are well put together and emotional, but others are full of problems. Anything with the magic Kai Leng in it truely sucks. Folks if you have a friend that is in a fight you do not stand a watch the show. Whoever was tasked with writing the scenes with Kai Leng needs to stop using tired bad action movie tropes, like puting a gun to someones head. That is a good way to have that gun taken away from you. There is such a thing reaction time, not to mention that anyone with any gun training is told not to get withing a certain distance of the thing your aiming at, for many reasons.
One last thing about story and that it is obvious that the writers know very little about the military. Inconsistancies in uniform, rank and standard military protocol is a bit grating to those of us who have served. (Okay I can't really speak for anyone else but it annoyed me.)
Combat: When it comes to combat I have to give this to ME3, that is inspite of heat sinks which are a bad idea. The inclusion of big melee attacks was a lot of fun. The only real problem is the one button for everything. Crouch, dive, jump over something, run, interact with someing all on the same button? I don't think I can properly express my frustration with this. I can't count the number of times I've died because I stuck to a wall instead of running by it.
Minigames: This hands down goes to ME2. Their hacking and decrypting minigames are fun and make sense for that task. I just wished that they became harder as the game progressed. I can't tell you how much I hated the minigame in ME1. I ended up saving the game before each attempt at the Frogger game. (yes I really sucked at it.) Of course there are no minigames in ME3 and I think it is poorer for its lack. I don't see planet scanning as a minigame as there is no challenge in it. It was just a boring exercise. Football is a game, jumping-jacks are not.
Vehicles: ME1 by far had the best in the Mako. Was it perfect? Absolutely not. But once I got the hang of the controls it was a lot of fun. Not to mention for those of us who liked to explore, having a chunk of planet to do that in was great. Now I know a lot of people complained about the handling of the Mako and how the environments seemed to similar, well you don't chuck the entire thing, you improve it, which they did not do with the Hammerhead.
Leveling: I have to give this one to ME1. One of the biggest problems with the franchise is the leveling inconsistancy from one game to the next. It really shows a lack of planning. I've read several times that they had originaly planned for ME to be a trilogy, but each game seems to have been planned and executed independantly, with little to no thought for what has come before. If this had truely been planned, then there would have been a progression of advancing skills and powers from ME1 to ME3. Instead they completely scrapped everying from ME1 to make ME2. I really hate the scrap everything and start over convention.
Now I know that Bioware has said several times that with each game they don't want people to think that they "have" to play the other two, but wouldn't it be in their best intrest if people "wanted" to play the other ones. One of Mass Effects greatest streangths was its replay value (well until ME3). So if they can get the players attention with one great game they will want to get the other ones.
Inventory: Yes there are a lot of problems with the inventory of ME1, but I don't believe I have ever seen a complaint about Borderlands inventory system. It was very similar, gather a bunch of stuff and sell it for money to get other stuff. As a matter of fact one of the big selling points of Borderlands was all the bazillions of guns you could get. Again Bioware needed to impove the inventory system not scrap it. All the gear in ME2 and ME3 feel very homogenised.
Powers: Also best in ME1. One of the things in ME2 and ME3 that I find annoying is that all powers are on the same timer. Granted that timer is shorter than the individual times for each power in ME1, but I loved chaining together a series of power attacks. In ME2 and 3 mostly I have one power that I use the most and only level up that one. In ME1 you really had to make hard choices about where to spend you points. By the way there is no way to explain why diferent types of amunintion are now powers. I am glad that they fixed in ME3 the problem with armor making someone immune to biotics.
Now there is no way to "fix" any of the problems with any of these games, they are what they are. I can only hope that Bioware, or some other company, can learn from the mistakes that have been made with the Mass Effect franchise. They have told one of the best strories in video games, but its inconsistancies do drag it down. Really, I would have thought that they would have learned their leason from the Dragon Age 2 curfuffle.