First of all, ME2 is a great game, but I can't but feel that it has gone a little backwards in some ways, here are my suggestions:
*More engaging story- don't get me wrong, the character stories are all great, really deep, and help build up the universe that little bit more, but altough nearly all the stories were tied to the main plotline, it was thematical and subtle rather than finding actual plotlines that moved the story along. Like I can see how Mordin's mission forshadows the final choice but it didn't actually add to the main storyline in any other way. As a result the missions seemed quite disjointed and loose. Lost opportunities include the council's almost non evolvement, where things like finding a Reaper could have directly involved them, as well Legion appearing randomly rather than being forshadowed throughout the game, I mean, he has been stalking you.
ME3 should have a much more epic story, like ME1, where party members have alot more to say in each mission (aswell as DAO like banter). The character missions however were very well handled so maybe they could be involved, but double up as recruiting missions, e.g. we would go to our batarian squadmember's homeworld to broker peace between the batairans and humans and request their help aginst the Reapers, etc.- therefore directly beniftting the main story line whilst tieing off loose threads. The recruitment missions could go, and instead be tied into the main missions. Sure they were fun but the "Loyalty" missions could just be deeper instead (Think Kasumi size rather tha Jack size).
Picking up loose threads- ME2 did bring back quite a bit from ME1, but did skip over alot aswell. What ever happened to the Lystheni Salarian offshoots (mentioned in the novels), the tension between the humans and batarians (brushed over in Omega missions), the entire hanar species (having no lines whatsoever in ME2, but albiet they got quite a bit of exposition and Blasto), and how are the Reapers actually going to arrive into the galaxy with no mass effect relays? ME2 did a good job with what it did cover, but I hope ME3 addresses these issues. The emails were a good sytem but it was frustrating that characters would request to meet you and you never could- hopefully we'll be able to get that interview with emily wong, etc. and being able to interview back would be nice. I think my biggest fear is that ME2 left alot for ME3 to cover, the issues between the quarians/ geth and the humans/ batarians, whatever happened to those Protheans, what are the keepers, will the genophage get restored, etc. but then brought new issues to the table like who killed that Reaper, the illness of the drell, the state of all your squadmates who can all be dead, etc. and then there's the raloi, the yahg, the "ghost" race, and all the other implied countless races wondering around the galaxy,I just hope ME3 can tie up all these loose ends, if they're not resolved in ME3.
Misc issues- The female variations of species, expecially turians badly need to be included in the next game, possibly as squad mates so that there can be more females in the squad. The Turians themselves could use some more exploration, I mean Tali was practically a walking codex but we still don't know too much about the turians apart from the gem of the conversation (what, like one of three conversations you can actually have with Garrus) about the turian military. The hanar, volus, batarian and elcor could use alot of depth. Please can we have a hanar, volus and elcor crew mates, that would be impossibly awesome, with the added bonus that we finally have alien crew (with side missions like in ME2). A batarian squadmate is also crucial, since we still haven't had one yet, and he/ she could provide alot of depth to the race.
Hopefully ME3 includes around two new races, aswell as the Protheans (maybe). Including the Raloi and the Lystheni (or however it's spelt) Salarians would be great aswell, and would help expand the universe.
Planets- The homeworlds, e.g. Palaven, Sur'Kesh, Thessia, Kahje, the batarian homeworld, and the worlds (maybe colony worlds) of the volus and elcor (come on, seeing elcor with turrets mounted on their backs would be plain awesome, they NEED to be implimented into ME3), and of course Earth, Rannoch and the Prothean (Reaper?!) homeworld. I hope the citadel comes back (this time with the Presidium included) and Omega (with more levels) aswell as the cerebus/ alliance main ship/ station (complete with Vorcha living in the bowls of the ship and shops in the hub section).
Also- More conversations with party members, no more calibrations.... no more than two humans this time please, speaking of which, having a female turian/ salarian/ krogan/ batarian would be awesome, along with a male quarian.
Ok that's about it.