I'm LOVING this idea.
A great example of this type of arena mode can be found in the game ISTROLID.
Istrolid is a free shipbuilder/RTS that's similar to Cosmoteer although not as complex. The MP arena in Istrolid is very close to what's being suggested here and it's helpful to note how it went about things:
Multiple capture points work well (5+) it makes having some manoeuvrability more important than just concentrating your force in one place. But also makes kiting into a weaker tactic as it's hard to hold a point if you're always retreating. Most importantly though no tactics are ruled out completely, they all have their uses.
The arena is laid out a spawn point on each side of the arena (the arena seem to be infinite in size) with the CPs strung out in a rough line between them. The position of the CPs is slightly random, the might be clustered in places or they might be spread out a long way (vertically as well as horizontally), this slight randomness about the arenas helps keep each game fresh and the tactics less predictable. The arenas are also symmetrical in layout.
Matches in Istrolid don't take very long, usually between 5 and 20 minutes, some can go on for over an hour but that's very rare. Obviously, balance and the number of resources gained from capture points (CPs) will have a big effect on how long the matches take.
CPs can be captured quite quickly in Istrolid but they're not instant. This is important otherwise fast scouts could just zip over all the points and take them instantly. A delay of around 5-10 seconds works really well.
The win condition in Istrolid requires one team to take all the points, rather than for one team to lose them all. The difference is subtle but I feel like its important.
Each spawn point has one CP located next to it, these starting CPs give each player a defensible "base" to work from. There is full visibility all the time in Istrolid (apart from cloaked ships) and the spawn points don't move, you can usually have time to spot advancing ships which give defenders a little advantage. although the closer you are to the opponents spawn, the longer it takes to get reinforcements.
Istrolid has a quick-bar at the bottom for ship selection, it also gives you basic stats for each ship. But you can redesign or create whole new ships mid-game if you want, its risky because you have to go to the design screen and you can't order your ships or observe the enemy while your building something, but sometimes its good to have that option in case you come across a situation you didn't expect but you know the fix is a very simple design adjustment - fast engineering is a skill and I wouldn't mind the option being included. That said, I don't think altering a ship that has already spawned is a good idea, otherwise, people will just build a titan, and keep on adding more stuff to it as it advances, even mid-battle, and just steamroller the opponent.
I'm really excited about this arena mode, it's going to be much more interesting than simple deathmatches.
Love the idea of having "motherships" as spawn points too.