1. So I'm stuck to replaying maps I already designed. I can handle that, but maybe I can have a random rotation of them to keep the variety level elevated. Is that even possible?
2. I already know starbases can replace planets as population centers. I was asking more about totally replacing planets. I know they can be made to build frigates, so I would think they can also be made to build capitals. Resource collectors would all be neutral in this mod, so even with control of the planet you wouldn't necessarily have any resource gain. The true mothership is basically the Flagship concept meets the Starbase concept. A capital ship that is larger and more powerful, but is unique and triggers defeat conditions if lost.
2a. I already know how to avoid the research structure issues. Simply remove the need for the research trees to need structures, but increase the costs to compensate for the lack of needing to conquer planets.
2b. Can a capital ship be given an ability that will change it into a starbase and the starbase have its own ability to change back into the mothership? Losing it in either mode would result in a defeat condition.
1. Not necessarily. The random maps are not hard coded, open one up with notepad and see what I mean. Granted its not as flexible as I hoped, but you might be able to hard code the home planet positions as with a normal map than use the randomization parameters to handle the rest. Also you can set a spawn probability on phase lanes and planets, so you could also use that to increase variability if the other method proves too difficult.
2. Okay, totally replacing planets is impossible. For one you lose the game when you don't have at least 1 planet under your control, end of story. There is no way around this. Also I'm afraid there is no way to trigger when a game is lost, only when a player looses all of his planets or a player gets the required number of diplomacy points (if diplomatic victory is enabled) can do that. I'm unsure if starbases can be made to deploy capitals.
2a. Well that would work, but it would be tricky to balance.
2b. Not really. For one, capitalships cannot go directly to starbases, only frigates can do that (but as abilities can spawn frigates there is a way around that). Further starbases cannot really revert either, the best you could do is make the starbase spawn a frigate that has an ability that calls in a capital ship (using returning armada code), then have both frigate and starbase destroy themselves. This would be a bit crude however, and it would take a bit of time for the capital ship to phase jump to your destination. Also all capitalship levels and starbase upgrades would be lost. This is why its easier for the mothership to just spawn frigate intermediaries for this kind of thing which then turn into starbases rather than the using the capitalship itself.
I know its probably not exactly what you had in mind, but you could use the needing to have planets alive to your advantage. If you give the motherships the only colonizing ability in the game (and give planets low health), it would be quite easy to build a handful of siege frigates and size the win. You could also give the mothership the only planet bombing capacity, effectively preventing you from eliminating another player if you lose it (if you also got rid of Novalith's and other abilities that damage planets of course), though the AI won't recognize this and thus still resist even if you defeat its mother ship.