I mean the reference applications.
Hard to say what RIM will and won't fix in the coming months-- they don't generally share that with us, much as I'd like them to I don't find the rotation is horrid on the Storm but it does rotate too easily.
The Storm has just EVDO (Verizon's version of 3G) while the Omnia has both EVDO and WiFi. That's a plus if you'll be using the device near hotspots at work (assuming you're in an area of the hospital where wireless is allowed) and home. It's a bit faster, though the biggest plus is for those who don't want a data plan (moot now that Verizon requires a PDA data plan with these kind of phones) or if you're in an area that lacks EVDO coverage.