I wonder if Speilberg would do it...but he's never directed a sequel that wasn't to a film franchise he started, or in the stuff adapted from books, done the first one. Tyrese Gibson suggested Spielberg as a choice, but we'll see.
I could also see Joe Johnston (Captain America) or Stephen Summers (GI Joe-another Hasbro property-and the Mummy films).
One thing I'd like to see them get rid of is the 'macguffin'. TF1 had the Allspark, TF2 the Matrix and TF3 the moon stuff. I'd stop trying to make these films too much like Indiana Jones or National Treasure that way....it kind of made the backstories way too convulted and contradictory. (Although IDW has been trying to sort that out in their movie-based comics with some limited sucess).
Also the same could be said of the 'ancient transformers'-Sentinel Prime was too similar in MO to The Fallen IMO.
Also there's the question of how they're going to bring back all the Decepticons that got killed off. Granted, they did bring back dead Transformers before (Megatron and Prime in ROTF)...maybe they can make Megatron into Galvatron, his rebuilt (and even more insane) incarnation from the later seasons (and animated movie)? or even have Starscream's remains become Cyclonus or Scourge (Since outside of the toys Thundercracker or Skywarp were never introduced).