Whelp, here we go again!
Don't worry, I'm giving MP the benefit of the doubt, so first and foremost, welcome, good luck, and here is a beer glass raised to you for taking up the torch. Props to starting from scratch...erm, again...with all of this, and I sincerely feel whatever you produce will be an upgrade to what we have available now.
Annnd now to the ideas/comments/input.
Gameplay:
I'm with Burn as well on this, dump the regular missions and lets just see the map missions and challenge arena. I would definitely love to pit fights against individual players, esp if we can fight within our own faction. Just something to really rev up the competitive gameplay AND we wouldn't be limited to fighting the opposition (in the arena).
With map missions, frankly if its only 2 factions at the start, I'm fine with that; lets get the game out and then worry about adding in more factions and the like.
Graphics:
Definitely some Alt updates would be nice, and I'm sure the community can help with that one. I think we had a huge rally last time we did this, and it worked out great, so why not again?
Logic:
For the love of everything please start from scratch on weapons and armour. Having to dig into linear algebra just to figure out what the stats were was frigin' ridiculous! My vote would be basing it on a simple formula from an already existing structure, such as D&D, so people can do the math without too much headache.
Also, a full listing of what item gives you what stats would be a great plus. Not having that listed I think turned off some people because they couldn't figure out what weapon gave you what kind of stat +/-.
Speaking of +/- stat mods, that would be a lovely addition. For example, a fusion cannon would be a +8 hit, however also giving a -3 speed and -5 recharge. (Granted this is just an example, I am not aware of what stats you are bringing into the game and how.)
Just my 2 pennies.