True, when you look at the big picture, the main game isn't that canon breaking, not in the way that you can just put a finger on it and say: 'Yeah, that ruined it.'
It's about all these little, subtle details that often go unnoticed - thermal clips for example, bothered me. They are a good addition, mind you, but as far as it goes in-game lore, they were introduced after the Battle of Citadel, and on many places during the game (mostly side-quests) you can meet (and fight) with people/machines that have been out of contact with outer world with more than a decade, but are using cutting edge technology and weapons. Nitpicking, yes, but it could have been fixed or dealt in another way.
As for other canon-breakers, as you point out, they are on line with regular canon-breaking in many franchises, but can be quite annoying, as they often employ quite radical re-design. Cerberus, for instance. Albeit just presented from the other side, it still sometimes feels like BioWare really went over the top with it, when you compare it to how they were presented in the first game (I think someone used the term 'Nazis of the Galaxy' in some earlier discussion). Again, hard to point where exactly BioWare went wrong - they crossed a line on many places. Didn't make a big crossing, but still a crossing.
I agree that characters are very good. Few of your squad mates are some of the most memorable characters you can meet in games that have recently been released (I still laugh at Mordin performing Gilbert and Sullivan).
Dialogues are generally better written, and I'm not sure if that's just me, but that wheel caused more problems than in the previous game - the text that is written in it, and what Shepard actually says often seem to go in quite different directions.
As for combat in general, it is vastly improved - more fluid, faster paced and less frustrating - except for the auto-heal. I simply don't like it and I think BioWare did a better job with it in the first game - Medi-Gel heals, Unity brings the fallen squad mates back (if I recall right). This new Medi-Gel/Unity...union is just too much.
However, everything else about the combat (and every little detail that goes with it - from picking guns to customizing armor) is a superb.
