If anything, the extended cut strengthened my belief in destroy being the best ending. One of the best things the extended cut did was clarify that the catalyst is just another crazed AI and not some sort of mystical god-like being, which makes it more important than ever that it and its machines be destroyed. I can see why some would pick control though, if they had played a paragon Shepard and were certain he would never use the Reapers for evil. I can understand why synthesis seems tempting when first mentioned, but I still can't stand it from an ethical or thematic standpoint, so the extended cut hasn't changed my opinion on that at all.
My primary Shep is mostly paragon and is the type who I'd be least worried about picking control. Unfortunately, the way I roleplayed that one, control would have been the third of four options. (Destroy, reject, control, synthesis in that order).
For that one, the decision probably makes more sense in the EC ending as the Catalyst does mention that things can be repaired and she was praying that it might include EDI and the Geth under that heading.
Reject would have had her praying she'd brought enough firepower, but doubting it.
Control - She'd have worried about getting corrupted by it all once she'd lost everyone.
Synthesis - Forcing that large a change on every single person throughout the galaxy?. It just didn't feel right.
For my next Shepard, control will probably be the main option and the galaxy had probably better behave itself