Most importantly...
* The three bugs listed in my signature.
* As many other bugfixes as possible.
* Support for the most common host applications.
* Improved stability to a level where you can use it for live performance (from what I can tell, this has mostly to do with memory management issues; S|M doesn't seem to deal well with memory-to-disk swapping).
I can't stress enough how important it is to have a solid foundation before adding features.
As for features, I'm really looking forward to having the audio device selectors available in FlowStone. Since they already exist, I'm assuming they'll be in the next release so no point in putting it on my wishlist. Other than that...
* The ability to disable the zoom and use the scrollwheel for something else. (I'd rather have the zoom functionality removed completely from the editor as well, but that's unlikely to happen.)
* Ability to disable the menu in compiled .EXE's completely. Perhaps Flowstone can already do this?
* More ASM commands; this should be trivial to implement and allow the developers to create many of the items on other people's wishlists.
* Shared memory for the poly's; basically like the blue memory write, but for polies.
* Better multicore support. S|M only seems to use one core, even though it has atleast two threads. I don't like my sound getting choppy when it's only using 50% of total CPU performance.
Obviously many more additional features would be welcome, but I'd be more than happy with just the first list.
I wouldn't pay for an upgrade if the first four points weren't addressed properly.
I'm pretty sure most people will gladly place those points prior to whatever wishlist they posted here, albeit with perhaps a different preference as to which bugs to fix first

It's rather pointless having cool features when the platform they depend upon isn't dependable.
In fact, forget all the previous stuff; here's what I'd pay for:* Bugfixes
* Stability
* Compatibility
AFTER those are addressed, I'd gladly pay for features. But until then, new features are just a waste of time AFAIC.