I recognize that being tied to the ST engine will limit to some degree what can be done with SS2. Some features that are common in synths (e.g., arpeggiators) would be sort of useless in ST. So I recognize this issue, and I'll keep most of my suggestions fairly general, but this probably won't stop me from making impractical suggestions.
Anyway, here are some of mine:
(1) More types of filters, and greater flexibility in using these filters. Also, it would be nice if the extra filters in the effects section could also be tied into the LFO's.
(2) More ways to create movement. Other than the LFO's and a couple of the effects, there aren't many ways to create movement in the sample you're working with. It would be nice if there was some way to trigger various individual sounds at different points in time while playing a combi. It would also be nice if there was some way to cause sounds to repeat. Some of the samples have this built in, like some of the repeating percussion sounds, but it would be nice if the user could create his or her own tempo and pattern.
I'm sure I'll think of more later, but I'll let others chime in now if they have any.
