Not an awful lot at this point, WMC. Most of it's minor stuff that can either be worked around or is more presentation-related.
It'd be pretty handy if the engine could play more than one play-sound-from-file at once. I assume there's a reason for that limitation, though.
You can't play regular messages while using cutscene bars, because the bars obscure that part of the HUD. This one's a bother, because it's only the top half I'd want below the HUD - if the bottom half was also beneath it it'd make cutscene transitions look dodgy.
Show-subtitle isn't as useful for storytelling as it could be at the moment because of the fact that, unless it's horizontally and vertically centred, it won't compensate for different resolutions. I think it'd be a far more useful feature if its positioning was based on percentage or something rather than number of pixels.
Like I said in another thread, you can't do subspace transitions yet. Neither can you have storms in subspace. I know that second one's been brought up a fair few times, so I don't have high hopes for its feasibility.
I'd like to see a 'countdown-start' SEXP that functions like supernova-start, but also allows you to set the text to display beside the countdown and doesn't do any of the supernova things like enlarging the sun and killing the player when it reaches 0. Plus another SEXP that can stop the countdown. And a Status SEXP that returns the state of the current countdown! And a pony!
That's all I can think of at the moment.