There is only 1 way for this new version of MOO to be better than SD2. They need a development staff larger than one person. I'm not sure if thats possible
Owning both SD2 and GC3 (and never owning GC2 or SD1, almost 2 decades since I played Civ or MOO), it really comes down to play style. Both games have some very unique features, which are great. Both games have some pathetic downfalls, which are sad. Replayability is quite important, and GC3 wins that by a landslide IMO.
I disagree with the GC3's devs thats combat cannot go RTS. They would just need auto-battle resolutions to be fairly close to the AI's RTS battle skill (which may be a challenge). In SD2, the auto-battle resolve is horrible, forcing you to play battle RTS. Its so bad, that in SD2, in RTS mode, you can just not move your ships at all and always do better in RTS mode than auto-resolve. But, the fights dont take that long, in both games I spend much more time planning and executing empire decisions per turn, than battles. GC3's ship designer is fantastic, but its only for asthetics, and I realized WTF am I spending so much time making ships look cool, when it doesnt matter for game play.
If GC3 added SD2's ship design ability and RTS fighting, it would be hands the best. GC3 has already overcome the SD2 downfall of ridiculously large fleets, due to its logistics system (which can itself be a flaw, due to a well designed Uber Fleet destroying dozens of fleets and taking no damage). This BEGS for RTS, as its not a lot of ships to control. Of course, both games struggle with land combat, as its a SPACE game.
Turn based is the least of my worries, as star wars empires at war was fully RTS, and you simply spent most of the game on pause turn based also lets multi-player be quite viable. As well, the hex system isnt an issue at all, in fact, much much easier to figure out range based situations. EXCEPT I AM F-ING TIRE OF COUNTING HEXES. PLEASE ADD A FUNCTION WHERE ALT+LEFTMOUSE SHOWS DISTANCE.