I for one read nearly the entire codex while playing ME1, and it all made the universe feel more fleshed out (and I just like flavor text like that). It felt like bioware had really done a great job creating a massive and (semi)believable world to play in.
Then ME2 came out and so much of it felt wrong. Now all these guns that I had used before need stupid clips?! None of my teammates wear armor?!?!
The thermal clips I understand and even like a little, over-heating was annoying in the first game, but letting Miranda and Samara run around like they were booth girls at the 2190 Adult Entertainment Expo just seemed like the worst kind of pandering. It would have been fine to let them strut around like that in the streets of Omega or Elysium but nearly every combat sequence started with a load screen, if they had appeared on the other side of that load screen in personalized armor I wouldn't be anywhere near displeased enough to rant like this. The mechanics of the game wouldn't have needed to change, I don't care what my teammates are wearing as long as they look ready to take on a geth colossus or had the common sense to put on something more than a filtration mask in the utter vacuum of space!
There was a planet in ME1 that wasn't very important to the plot but the flavor text described it as having spores throughout its atmosphere that sent humans into anaphylactic shock immediately, so whenever you stepped out of the Mako everyone had their masks up. I remember thinking "hmmm that makes sense" but whenever I saw Miranda walking around with that mask on (which doesn't even look like it seals correctly) I thought "why aren't you suffocating or freezing to death or exploding or any number of gruesome things."
TL;DR: I don't really care if Bioware changes things from sequel to sequel, its their game. But some of the changes in ME2 just seemed like low-level pandering and lessened the experience for me.