I am guessing that this is the actual name now of last years 'not-MoM' game that saw much speculation...it's been awhile since I've looked into this game as you can tell. Taken with all due respect to the OP that this game, while similar, is NOT MoM 2 or a remake of the original, I feel that some of your worries are likely unfounded.
1. I have played many many 4x and RTS games, and while having lots of factions is indeed nice, I have fond that I far and away prefer fully fleshed out factions over quantity anytime. And that seems to be the direction that is being taken here. Also, as has been mentioned, faction development can lead to many different end results giving us even more variation and flexibility than from more constrained faction selections. Add to that the undoubted modding that will go on, as well as the clear, at least to me, intention of adding more faction material with add-on releases, and I think this issue won't be as critical as it may seem to some.
2. I have to completely agree with your 2nd point. The most important decisions you make in any game of this kind is before you even begin playing. Thus, the more options available at set up, the greater the variety of game play options and strategy, and ultimately the greater the longevity appeal of the game. It does seem though that some of these types of set-up decisions will come into play early on in each game too as you create and use your hero characters and I think that will lead to the same kind of variety that you were referring to from the old MoM set up selections. Still, the more variables that we can manipulate during set-up, the better for me...and the more of a headache for the testers...
3. The spell quantities I am less sure about, but considering what they've done with the tech tree stuff in GalCiv, I can't believe that they would be lacking in choices in this department, especially if you can craft your own unique spells. This ability to create your own spells alone can lead to a great deal of fun and experimentation.
All in all though, I think as the OP also realized that we are just speculating on alot of things at this point. I too, long ago, was burned by the travesty of MOO3, but I don't think there is cause for worry here. Considering that again, this is not a remake of MoM, and also the great deal of enjoyment and long hours I've spent with the GalCiv series with its many variations and nuances from these same folks, I'm not concerned at all that they will drop the ball horribly here, as was the case with MOO3.