first of all, i would like to see Tali's face
since ME3 will be last, some marriage is in order
more racial species interaction
let us visit home worlds of Turians, Asari, Salarians
let us help Quarrians re-establish their home and help them negotiate or make war on the Geth (depending on the so far scenario, where Shepard said either go to war or make peace)
do NOT make a default start in new game, I was so annoyed I have totally no control over who I left to die and saving/not saving the council, utter crap.
let us buy weapons, AND make new ones or improvements.
ammo back, please,
changing armor/weapon in the middle of a mission
grenades, soldiers are useless without them IMO
PRESLEY IS DEAD!
let us visit Zu's Hope and other places from ME1/2
I wanna go have a sushi, but they serve it on earth I wanna go to earth please.
heavier consequences of the choices
improve the missile launcher, it's crap, grenade launcher is much more useful.
bring back the combat simulator
i wanna buy a nice moon and a house to it when I retire from the mission, when I beat the crap out of reapers, with my Tali wife and my half human half quarrian kids

make us do some research for quarrians to improve their immune system
make us of more use to the salarians and their culture, damn marriage among salarians is a silly thing lol
I wanna meet turian girls lol, let us visit Turian space to have us negotiate war efforts against reapers directly, the council is full of crap anyways.
fix the Council, they are full of crap, someone that knowledgeable and powerful should be able to tell what the situation is like, they were utterly useless in ME2, and they were of no use in ME1
since ME3 is supposed to be the last part, i think you should throw a huge load of stuff into it, the game should be at least 2x DVD9 content, to install, and the entire installation should probably exceed 20 gigs in the end.
make the DLC viewable and purchasable/downloadable from withing the game, like in DA:O
make sure you release DLC
ONLY when you are sure it is fully compatible and stable, the inability to save midway and exit game on DLC missions and then trying to load it and see it's
"UNKNOWN AREA" is seriously pissing me off.
Give us a few solo missions on other characters and sheppard, it would be awesome doing some solo missions to get to know better the characters.
Romance:
when I set my eyes on some character, some choices and actions during the missions should affect the relationships, For instance, I set my eyes on Tali, so from the very beginning I lacked the conversation with her about the first time we met in ME2, or ME1 even, when on missions, the way I treat tali for instance I help her out when she is under fire to buy her time to use a power or take cover should also slightly affect relations and topics.
I don't mind thermo-clips, but do tell in game why they went from overheating to thermo-clips, and why shouldn't I keep firing the gun without a thermo-clip, it should be possible, but at a very low rate of fire, this way it makes sense, and use different thermo-clips for some weapons, assault riffles and shotguns should have different clips, also, you refer to thermo clips as ammo, which is simply wrong, i was constantly laughing at this blunder, at the start of the game you explain that thermo-clips prevent the weapon from over heating, then later on you refer to it as ammunition, the stupidity is beyond the scale here.
more interactions between the Geth, Legion and the Normandy crew and the outside worlds, I mean, the citadel should look into the Geth themselves, if for instance I convinced the Quarrian Admiralty board to negotiate with the Geth and it succeeded, the Citadel should also visit and negotiate to create the better future, common sense is not that hard and Bioware seems to think the galaxy is a stupid place for stupids.
Please do create more idiocy on leaders of the merc groups, Eclipse had how many leaders i killed ? and they were all Funders, or was it Blue Suns ? just how many funders do I have to kill ?
more powerful and difficult enemies, I had a lot of joy fighting the Shadow Broker alien dude, that fight was I think the only fight that required tactics.
Although I do not need to look at radars so much, don't make them as useless as in ME2, placement of your team mates in combat is crucial, if you do it right you don't even need a radar.