If your bro can make nice looking ship and race models, then I would agree, but with 2D, people who play those games don't expect or demand amazing graphics. It would make a distinct difference to everything. I mean, a 2D space strategy game is all about strategy, a 3D space strategy game has to be pretty too.
Personally I never got into the idea of 2D space, it should always appear 3D, so if you go for 2D - use parallax starfields and stuff to bring it out.
To make it 3D, you'd have to know 3D positioning and rotation inside and out - but it is quite easy to get up and running in 3D. I would consider making a 2D overview, like galaxy map, position of ships etc - then have combat done in 3D. I guess it all depends on what you want to do, the strategy gameplay itself will probably be more complex than the game engine, so I would experiment and see what you can come up with.
Maybe make a test engine for 2D and 3D, and see which one has the better feel to it.
Might be interesting to have a 3D turn based combat system - I think that would work pretty well, select what to do with your turn - move to another position, charge shields, fire weapons at targets, or warp the hell out of there. I played a turn based game on the DS a while ago which had this neat idea - what they did was released the turn based aspect when all the enemies are done. You would kill everything, then be left alone to quickly scoop up any treasure. Not sure how Final Fantasy that would end up - but I can imagine getting very tactical, surveying the battleground and deciding on strategies. This makes for easier AI, less of a concern for speed too.
One thing that annoys me with turn based games, is how often you have to tell a unit to move, if you want a ship to go somewhere, it should just keep going when it has a turn, like set the destinations and let the ships get on with getting there - while maybe your main battleship attacks - flanking, distractions, evasion. The more possibilities you afford the player, the more they will feel like they are in control.
I know one thing, comparing 2D to 3D - 3D is immersive. If you made it 3D, then you'll have much more fun developing it. It's really quite a cool thing to make your own environment and then explore it, and it's much more rewarding to fly around and with your teams creations.
I think 3D is the way to go but it depends on how you want your game to play. 2D can allow for really clear navigation, but 3D combat is so much cooler, and I think new teams need 'cooler' things to keep them interested. Know what I mean with that? - ideally your bro will be coming up with ideas all the time for ships and races and stuff like that - in 3D it's ideal, in 2D it's a little bit of a letdown. Spend a lot of time developing a ship design, just to have it shrunk down to a 32x32 sprite is not very inspiring - seeing a fleet of your ships fly by is pure inspiration for your team in comparison.
Epic just does not fit into 2D, and DBPro has a track record of making epic space games in 3D - just look at Starwraith series, and Dark Coders space game which won the last major TGC competition. You guys should have some serious brain-storm meetings, take lots of paper and each of you explain how you'd like the game to be played, then see what can be used from all the ideas. If you know what you need, you can research it and ask here for advice or even examples. Having a solid plan makes a project much much more likely to succeed and is vital in a team effort.
