Better:
1) Squad interaction. I love them moving around on the ship and talking to each other. It really gives the feel of them being a team instead of a ship full of loners. It also shows a different side of their personality you might not see when they're interacting with Shepard. The squad 'dates' were also great, lovely little moments of downtime outside the Normandy.
2) Combat. Much more fun than in ME1, and better than ME2 as well. I liked the weapon weight system, so we could customise our weapons sets completely, cooldown times, etc. Powers having two evolution paths that focus on different things is also good, and the fact that every member of the squad has a proper armour option (ME2 was lacking there).
3) Scope of missions. ME2 has a lot of missions if you include recruitment and loyalty, but they feel pretty short. In ME3, they feel really 'epic' and grand, especially Tuchanka and Rannoch. There are a few missions leading up to it, and then a big climactic finale. The fact there's an important, difficult choice to make at the end makes it even better.
4) Morality metre. The reputation bar was a much better idea than separate paragon/renegade bars. It allowed more room to roleplay abd mix/match your choices, instead of thinking "I have to pick paragon because I need enough paragon points to unlock dialogue X." It also feels more natural. Considering that renegade choices (especially) aren't that consistent in morality, it's better not having to lock yourself into one moral path or the other.
5) Squad and main plot. Except for Vega, arguably all squad members have an important role in the main plot, instead of just being tag-alongs. As far as other crew go, Joker previously had an important role, but now we also have a shuttle pilot, and a 'specialist' doing important stuff. They have a clear role and you can see them getting involved in the plot. ME1 had Pressly and Addams, but they never really seemed to be doing anything.
Worse:
1) Auto-dialogue. For the same reasons other people have said. It makes each Shep feel less unique, and gives less choice. DA2 was voiced, yet you always had three dialogue options to choose from. Sometimes, if you're giving an opinion, up to five. DAI offers even more choice there.
2) War assets. If you want to have stuff going on off-screen, then DAI's war table is better for that. You're presented with an issue, your three advisors offer three different methods of dealing with it. You pick one, wait for results. Who you pick affects the outcome. It has it's own issues, but definitely offers more interest and choice than scanning a planet and delivering item Z to Bert on the Citadel.
3) Forced emotions. Another suggestion from DAI! Their 'reaction wheel' offers a few different emotional responses. Something like that could've been expanded on and put into ME. That way you can choose how your protag responds. R.e. Thessia, Shep could've chosen from stoic, upset, angry, positive, confused.
4) The ending. I won't get into the stuff that's been mentioned on different threads a million times. But compared to ME2's suicide mission, Priority: Earth doesn't have the excitement, tension or badass feeling. Also, during the SM, we see the forces we've collected playing a part, which we don't much in PE.
5) Character creator. This one's pretty minor. The textures (especially for hair) were much better, but the eye colours often looked painted instead of realistic. The make-up was much more wishy-washy than before. Then there was female hair. If it was loose, it had a touch of 1960s bouffant. If tied-back, it gave her an oblong head. Weird design choices.