Loads and loads of autodialogue with extremely limited (and binary) dialogue options
The ending, of course, which is a red, green, and blue garbage fire.
"Follow the arrows" quests. (we'll see what MEA does for "exploration" this time). Not to mention scanning side quests so dull they make gathering ram meat look exciting.
I have to imagine that these things come down to the setting and writing. Setting the game during a presumably time sensitive war defined the tone of the game's design. It must hard to justify making meticulous and exploratory quests when the enemy is right in front of us with an army. The atmosphere just isn't conducive of the slower paced design necessary for deep RPG questing, and I don't think Mass Effect's writers were capable of writing themselves out of that box (not too many would be). That's why I think the move to Andromeda is going to be a positive change. If BioWare sets the tone correctly from the very beginning, then it's more likely that the rest of the mechanics we want will fall into place naturally.
If The Witcher 3 proves anything, it's that your game can have a bunch of repetitively designed quests as long as they have a good narrative hook and a decent amount of production value put into them. BioWare has the production value, so I wouldn't be too worried there I think what happened in Mass Effect was a marked decrease in mystery as the series went on. Mass Effect was always a fairly straightforward universe. It's certainly no Planescape: Torment, which has has a setting so esoteric that just about every task is inherently fascinating, and it never tried to go for that Star Trek "philosophical sci-fi topic of the week." This leaves the writers in an awkward position because grabbing those interesting narrative hooks in Mass Effect's style of universe isn't so easy. BioWare tried to supplement their setting with political drama, but I don't think they were entirely up to the task.
Again, setting is absolutely instrumental in the design of a game. It's instrumental in every media, but it might not seem as intuitive to think that a setting can have such an impact on gameplay. I think we're guaranteed a kind of domino effect from ME:A's focus on exploration and a strange new galaxy.
banter and the ability to mod weapons (put back in the game after being gutted in ME2) were the only real improvements.
Maybe it's just me, but I never thought that banter was reduced that much between entries. Maybe I just didn't care that much because I thought ME2's companions were more interesting in general.
But like I said earlier, BioWare switched their approach in ME2. Rather than give us a bunch of samey weapons with all sorts of unbalanced weapon mods, they dialed back and gave us fewer, more distinctive weapons. To continue my stealth game example before: ME2's design is closer to the optimal shooter/RPG hybrid. Stealth games work because they provide the player with a limited number of distinctive tools that can result in a greater variety of gameplay options. ME1 may have had a greater number of options, but I'd argue that almost all those options are entirely artificial: in the end, the action went down the exact same way no matter what mods you slapped onto your weapon. Maybe that's just me though.
A skill system barely more inspired than ME2's
Mass Effect has never had a good skill system. I don't care how many slots ME1 had, Mass Effect's leveling has always been bland percentage boosts. The sequels at least merged all the minute differences into fewer, more distinguishable tiers.
But again, stealth games have leveling almost perfect. Take a look at Dishonored, Deus Ex, or MGS5. There's barely a single item or upgrade that doesn't serve multiple purposes and won't distinctly augment your gameplay approach (less so in MGS5, but it's still amazing how good each upgrade is given the number of them). Action games just don't mesh very well with minute stat progression. That's by design: the minute differences in gameplay come from player skill, so the progression needs to reflect that. Ideally, each level up in ME:A would provide the player some new tool or augment an existing tool for a different task, but I think I can settle for ME3's leveling which at least did it's best to offer palpable augmentations to your powers at later levels.