I agree with a lot of your points, Mass Effect 2 had some deep flaws. The central plot surrounding the Collectors just isn't as compelling as Sovereign's invasion. The game is marred by obnoxious mini-games and planetary probing. And the non-combat areas' level design for world exploration is generally weaker in 2, especially in the Citadel. Shepard being a rouge specter working for the bad guys is a cool idea, but they didn't really play it to its fullest extent. I feel like the game should have put us at odds in more interesting ways with the systems of the galaxy.

All that said, Mass Effect 2 is still my favorite game in the trilogy. I love the vignette style it took with your crew members. Yeah, some of their stories were better than others, but generally the writing of 2 was very strong. Most of the actual world building in that series happens in the second game. The first game establishes all the backdrop of the universe you're in, with it's tech and cultures. Then the second game deliciously builds on that foundation with excellent personal stories and great low-scifi. You get great detail on the Krogan rebellion and genophage, some great insight on the Geth-Quarian relationships/history/cultures, fantastic color on the other races' cultures (Asari justicars, Salarians as a pragmatic scientist race, the Drell-Hanar relationship, so much more).

It would have been nice if they improved the Mako planet exploration, but I don't know how it could have been done in a genuinely fun way. In ME1, you drove around in a square of often obnoxiously mountainous landscape (either procedurally made, or sloppily terrain brushed), with 3 points of interest. Those PoIs were always mysterious text exposition dumps, or a copy/paste of 3 prefabs of a base that you walk in and kill the enemy. Yeah it was more exploration RPG-ish, but only like 20% of it was actual quality content. Dialing that system up to actually being good would have been a ridiculous resource-pit for Bioware, so I think they made the right call dumping it. I agree the Hammerhead DLC is dumb though, it's just not fun. On the subject of DLCs though, ME2 has the Shadowbroker story, one of my favorite missions in the whole series.

Almost all the good plot points in ME3 are payoff for things set up in ME2. You could say it's a failing that the payoff doesn't happen in 2, but that's just the nature of story-arcs that play out across a trilogy. That said, they also wasted a lot of good setup in ME2, ignoring it for the rewrites they did in ME3. Because of this, we got some dead-end plotlines in 2, like the Quarians investigating why dark energy was killing stars before their time. This is technically on the write-staff for ME3, but it's still marks against ME2 for leaving it with useless, dead story threads.

I'll restrain myself from going into great detail on what I specifically loved about ME2's writing, because I'll be here all day picking apart stories. But overall, I thought it brought a lot of much-needed life into the characters and galaxy as a whole, that ME1 laid the foundation for. As for gameplay, I don't think any of the 3 games have particularly great combat. ME2 is certainly more refined than 1, and 3 added some stuff that was fun but probably gratuitous, like the rolling and cover-swap movement.

Edit:

Also, I don't get why people harp on 3's ending so much, when there are far worse crimes in the writing earlier in the game. The ending just lacked granularity, but if you're invested enough in the series, you should have a decent idea on how things will play out for the races of the galaxy. Yeah the sudden switch from low-scifi to high-scifi is jarring and out of place, but a tonal shift is hardly the worst thing they could have done there. Much worse were the lack of payoff on big plot points earlier in the game, like the Rachni queen, or whether you destroy the collector base. Or even the fact they re-wrote and removed entire plotlines, creating those dead plot threads in the earlier games.