[ ] Extra Shuttlebay (+2 Engineering)
[ ] Main Cargo Bay (+3 Cargo)
[ ] Expanded Medical (+2 Science)
[ ] Science Labs (+4 Science)
I've got to say, with the fore of the primary hull to still consider, each of these do have some real merits to them. However, I do have my preferences.
As stated above, the extra shuttlebay seems like a big investment for some rather edge-case scenarios. As helpful as the extra shuttles might be sometimes, there are other uses that the allocated space could more usefully serve.
The main cargo bay isn't too bad of an idea either; in times of war it could carry still more torpedoes for what I'm sure are the very hungry launchers we have aboard, and when the war is over it means the vessel could carry larger cargos (though nothing on the level of the
Archer) at far greater speeds.
The expanded medical is also quite important in terms of combat usage, as any walking wounded can be patched up on-site without having to depend upon station or planetary medical facilities as much. After the war, hospital ship it might not be, but it would be able to sustain its crew for quite an extended period of time.
The science labs, at first blush, seem more like a 'planning for the future' sort of thing, but they would likely have an important use in the here and now of war: information gathering and study. The most powerful weapon we could ever have is the knowledge to skillfully apply our efforts where they're needed most, and whether that's a scan of a damaged ship or station to determine common failure points or places where we can attack with electronic warfare beyond our phasers and torpedoes or the in-depth biological makeup of Klingons in conjunction with the medical facilities (useful for both medical purposes and to detect whether they would be so brazen as to carry any biological weaponry on or within them), they offer far more use now than simply 'oh, we're Starfleet, so of course we're going to stick some science labs in there'.
So, when the vote comes, I'm actually going to advocate for Expanded Medical and Science Labs. They synergize quite well in many respects, and our information-gathering capabilities should be nothing to thumb one's nose at.