Haven't gone through the whole of this thread, so I don't know if what I'm going to say has been touched on, but here's what I'd like to see:
better customisation items:
More hair, as the 50 shades of skinhead from DA:I was just annoying, perhaps even long hair, for both males & females
Full beard option
tatoo's, both facial & body
scars, both facial & body
Squad options:
Customisable armour like in DA:I yes everyone had their own style, but you could swap bits out to change the look & stats, as well as change the colour.
Better AI, with how basic is was in ME3 it was more annoying than helpful, I lost count of how many times I would tell a squadmate to use a specific weapon or power, only for them to decide not to, this leads me onto my next point.
Choice of behaviour, the choice to set your squadmates to assault or support, that way a sniper character set to 'support' would hang back & use their rifle, maybe even choose whether they focus on strong or weak opponents, thus allowing you to take a more strategic approach to combat.
Conversations:
Like in DA, give us some form of emoticon for our dialog choices so we can have a clearer understanding of whether we're about to make a joke or drop out a flirtatious like
randomise the location of the paragon/renegade lines, as it's too easy just to say, 'I'll say the top line everytime.'
Weapons:
More customisation options, parts, colours, things like that
location sensitive hit boxes, ok so we have headshots, but aside from that, it's easy enough to kill a guy by shooting him in the big toe, bleh.
Powers:
Once again, ripping off DA:I here, but have certain locations on maps that require certain powers in order to bypass?
Mako:
It plays music while exploring with the option to choose tracks.
Ok, that's all I can think of, some might make more sense than others, still, it's just my thoughts.