Personally I would like a sequel set (at most) 25 years after the events of ME 3, and I would love to see my choices reflected in the game, but I would much rather Bioware cut their losses and not have a save import feature.
All of the choices presented in ME 3 are too big and varied to possibly be accounted for in the next game, without releasing 12 different copies, each built around one set of choices. Obviously the endings would play the biggest part, but like others have said, the fate of entire species are decied in ME 3, and unless Bioware is going to write 6 different narritives for ME: Next, you are going to be looking at your choices being either trivilized: "You sabatoged the Genophage Cure, but the Krogen 'grew out of it' and/or another random scientist was able to create and distribute the cure." Or you are going to have events completely retconed and cannonized thereby invalidating the purpose of having a save import in the first place.
Things like the endings would have to be address the most though, especially if ME: Next is going to be set after the events of ME 3, and no, I don't consider: "Have the sequel take place 10,000 years in the future, and just have the Reapers (Control & Synthesis) leave because [Reasons] and have the effects of Synthesis 'wear off' by that time." a valid method of dealing with the endings.
For starters, setting the game 10,000 years or so into the future means that ME: Next is only ME in name, everything that made Mass Effect Mass Effect would have changed by then (unless you consider ME to be similar to WH40K or Star Wars, in that technology NEVER advances). I mean imagine if you had an RPG set on Earth in 8,000 BC and then had the next game take place in modern day, its a completly different setting by that point.
As far as Control and Synthesis go, I didn't like them (Pro-Destroy), but I can respect the players who do, and whittleling their end game scenarios down to: "The Reapers left." and/or "Green stuff was the ONLY thing about Synthesis" would be a disservice to those endings and the galatic state they left the ME universe in. Synthesis is portrayed as the end of organic/synthetic conflict and EDI's narration durring the slides suggests that incredible advancements and understandings are taking place, and that immortality is within the realm of possiblities. Setting the next game in the far future WITHOUT bringing these events into account with mean that Synthesis is effectivley ignored. And don't get me started on the: "The Reapers just leave." scenario that is brought up about having Control and Synthesis carry forword into ME: Next.
The whole point of Control was for the Reapers to police/protect the galaxy, why would they leave after Catalyst-Shep says that s/he/it will defend and protect (or control if Renegade) the galaxy at large? And if the Reapers are still around in ME: Next, how can you have political dealings, and race wars if the Reapers are on standby to lay the smackdown on anyone that decided to get uppity. Synthesis Reapers were all about sharing their vast knowledge and intergrating with overall galatic society, why would they leave? Reapers are immortal machines, with more power than the entire galaxy combined (minus the Crucible), so just having them leave is not an aceptable method of bringing the Control and Synthesis endings forward, and would therefore the game would have to be dealing with a Cannonized Destroy or parallel universe.