Whether it be a prequel, interquel, or sequel there's problems Bioware will have to get around, to wit:
Prequel: The history of the Mass Effect universe is already pretty well established, so anybody that's played the first trilogy is going have at least general idea what's going to happen (this is one of the reasons the prequel trilogy of Star Wars was terrible). Also, and more importantly, in a series that emphasizes choice, having an already decided history will GREATLY limit those choices, unless Bioware is smart and just says "screw it" and makes several noncanon paths in addition to the canon one.
Interquel: Same problem as the prequel, but choices would be even more restrictive. However, this might actually be a good idea, since an interquel would be able possibly create another set of alternate endings to the original series that the future sequels could then run off of, (in short, a retcon trilogy) solving the ME3 endings issue. The could even go the parallel universe route for their sequels so that the original trilogy doesn't end up being pointless.
Sequel: The problem here is either things must take place a long time into the future so that the events of the original trilogy will have been forgotten or at least don't really affect things, or a canon choice for the ME3 ending will have to be chosen, either will probably piss fans off. The other problem is that they will have to create something EVEN WORSE than the Reapers as the bad guys, (and the Reapers as threats set the bar massively high) that antagonists make must escalate with each sequel, otherwise the audience won't take the threat all that seriously. In other words, if the Reapers are beaten, if this new evil is weaker or the same then what chance does it have?
Regardless, Bioware will have to do a LOT of work to continue the francise from this point on, it won't be easy for them. I'm personally in support of any of them, but I think the interquel retcon idea that I mentioned is probably the best idea