They won't be doing the Super-Extended cut of ST:TMP (the first one) because all the new effects were produced in SD. Short-sighted, that. Also, all the restorations to the other movies were also done in SD. That's why they are leading with the theatrical versions.
I am a little bummed that at this point I can't pick and choose which movies I'd like to see. Star Treks 1,2,4,6, and First Contact would be the only ones I'd buy, and 1 is sort of iffy. So I'll start with the 2-3-4 set and when the others are available individually I'll buy those.
I was just about to put up a note to let folks know, and/or remind those that are considering either of the sets that they are sets only and you can't mix and match.
As you've noted, there's a Genesis story arc version (II, III, and IV) which is much less expensive (approx. $50 retail), and the complete set (I - VI, with some bonus material making an extra disc) which will be approx. $110 retail.
Amazon should hopefully have some nice discounts (as would other places, such as DeepDiscount.com, etc.), but it's still not going to be all that cheap and there won't be any mixing and matching short of people buying sets and selling off pieces (which is not all that likely to happen).
I might, just might, fall for the Genesis arc version, but as noted it's all Theatrical versions, rather than Director's cuts and sooner or later Director's cut versions should show up.
That all said, (don't laugh please!), I'm really most interested in snagging IV, and am not rushed at all to get the others. If I saw that one split off by someone, I'd probably just snag it by it's lonesome.