@ptarth: That is... wow.
I have to say, it looks more complicated than it is, in the main, but at the same time it has a LOT of divergences from the core flow of the game that this is a sequel to. On the research problem, I think we're agreed on those being joined up.
When it comes to your suggestion, I feel like there are too many little edge cases and potential GUI snafus in there. How do I know which fleet a ship is assigned to, for instance? And a whole host of other display problems that I see going along with that.
But there's a lot that I like, so let's see if we can distill some elements out of that which are less radical but get at the same ideas:
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1. Okay, so first of all, we're all lately talking about "techs don't upgrade one ship, they upgrade an offensive and a defensive one."
2. Secondly, this thing of fast-travel keeps coming up. Overall I really don't like it... EXCEPT I really liked how you mentioned that basically there was a conduit to/from a planet and its flagship (in your design where every planet has a flagship), and that conduit was only good for the fleet ships and maybe starships. This solves the Small World problem I was concerned about, while allowing for reasonable logistics. Having it feel like your flagships are stuck way out behind enemy lines, but can shuttle smaller guys back and forth is... cool.
3. The idea of having flagships that are associated with planets is something that appeals to me. Not... exactly that thing, but something close. I'm not sure what feels wrong about one flagship per planet, but it rubs me slightly wrong at the moment. That seems too overpowered, for some reason. I love the idea of these mobile conduit ships, though.
4. For me... if we had conduits along the lines of -- hang on, I just had a brainwave.
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The AI is always warping stuff in from outside the galaxy, right? Or at least from "places unseen." What if the players could do that, too, only better?
1. Make it so that only space docks can build fleet ships.
2. Make it so that building fleet ships is a lot slower.
3. Let players build however many space docks per planet, like piling on more engineers in AIWC. But have it cost a lot of power there.
4. Have constructed ships either be set to "pop out here" or "pop out at x flagship or the Ark" or "wait in storage."
5. At any flagship or your Ark, you can immediately -- from the Ops tab -- dispense any ships from storage, at that location. Boom, fast travel. Dispense exactly the number you want.
6. The ability to scrap ships is removed. Instead, when a ship would be scrapped, it is simply sent to storage and you get nothing back. It's ready to be redeployed somewhere else, instantly if need be, but they're in the same state they were before (if they're shot-up, or engines-out, fix that before sending them to storage).
7. Pulling more from Magnus than anyone else: On the build tab, or something of that nature, on each planet have a thing that says "if there are fewer than n of unit x on this planet, dispense from storage until the quota is met." And another rule, optional, that says "if there are more than m of unit x on this planet, put back in storage until we're no longer over-filled."
Something like that?