I read something that claimed it'd be available in both versions, but I don't know if that was official. They hadn't decided, then, if they'd also offer a version that was cropped to widescreen.
I hope the new ship effects will be improved before they release it, but they aren't giving themselves much time.
The TOS dvd's are pitiful compared to the film. They used to sell film clips from the dailies, and I've seen loads them projected.
(In contrast to the dvds of TNG and most seasons of Voyager & DS9, which were taken from the crappy broadcast master tapes).
The TOS dvd's are not a decent preservation. Look at how they botched the barrier effects on the viewscreen in Where No Man Has Gone Before". Look at all the faded scenes. Terrible transfer. Not as bad as the GOUT, but pretty bad. Artifacting is bad, too.
The HD remaster, of TOS, is awesome. It looks like the olden days, before the faded prints & piss-poor transfers. (Even the 35 mm prints that they struck for syndication, back in the 80's, looked faded). The cleanup of dirt doesn't ruin the authenticity, in my mind. The new transfer is infinitely more accurate.
Also, the film used for TOS was much more fine-grain that that used in the new serieses, making it perfect for HD. Reviews & screenshots of the XBox downloads of TOS HD and Enterprise HD show that Enterprise's film scenes are softer. The same will be true for TNG, Voyager, and DS9. (The film-grain part is confirmed, for DS9, by interviews of the production staff of Trials & Tribbleations). They will, of course, have to be re-special-effects-ed, or at least re-composited because the visual effects were done directly to tape).
If they used a 3-pass transfer scan, for TOS, then the space-shots should look quite good, as they used to, back in the day.