The endings imo are what opened the flood gates. ME2 had its fair share of problems with...
Hub worlds being smaller with less in them.
A lot of party members that got focus during their recruitment, loyalty missions and Normandy conversations, but didn't say much outside of generic battle quotes
Having the least amount of powers
Lazarus Project totally shattering the lines between science fiction and just pure fantasy
Lesser main story arc than ME1
A more linear mission structure that had a set way to complete them, where ME1 allowed you to take different routes to solve the problem depending on morality
A more complicated paragon and renegade system that wasn't clearly explained
Not forwarding the overall ME story arc enough, which paves the way for the implausibly convenient Reaper off-switch
However the game goes out with an absolute bang with the suicide mission which, if you do it without a guide, is nothing short of nervwracking wondering how many people are going to make it, and who should be used for which job (with hints spread out throughout the game that only a keen eye would able to catch, which meant actually learning your crew and their strengths and weaknesses). Heck, even the final boss of the game is one of the laughing stocks of the series, but people look past it because of a satisfying ending.
Maybe they couldn't change a lot with an extra few months of development, and maybe the ending stays exactly the same. But Priority: Earth is by far the worst mission in the series, even as someone who will defend the endings until the end. It's linear, it's quite short, it doesn't challenge the player beyond a "lets throw 100 Banshees at the player for the obligatory massive horde mode" final push a lot of games have, and your choices don't change how the mission is structured. It would have been better if Shepard was allowed to command certain forces, depending on who is around, to do different tasks. Imagine having spared the Rachni Queen and the Geth, and being allowed to choose who joined Shepard to complete task A while the other tries to complete task B, which would result in group B's annihilation. You would then get to fight alongside who you chose as you took down that 100 Banshee wave. I'd love to watch updated Rachni AI fight against Reaper ground troops with Shepard. If Bioware could have done those things with the final mission, I doubt the backlash would have been as bad. Then again, a charity group wouldn't have gotten some nicely colored and baked cupcakes. At least the irrational backlash produced some good in the community.
I mean thanks to the endings we'll never hear the end of how awful people think the writing was (translation: things didn't happen the way they personally wanted), auto-dialogue, choices that didn't matter even though arguably they never mattered much beyond a few changes here or there. Oh, and completely nonsensical claims that ME3 is a Gears of War clone that somehow has less RPG elements than ME2 (huh?) that leads to irrational fears of ME:N being a CoD FPS clone (what is this I don't even...)
You know, despite classes having far more potential for specialized and unique builds. A huge arsenal of guns that have their own unique situations where they excel at or fail it which adds an element of pre-preparing for a mission which also plays into creating unique builds, compared to ME1's awful inventory system and leveling system filled with boring passive boosts which means the second you unlock a power it stays the same for the rest of game with no real sense of evolution or progression. Don't even get me started on multiplayer and how it massively extended the variety of powers in the series that will hopefully make their way to the SP campaign without needing mods in ME:N.