OR have some kind of maintenance cost in crystal / metal per ship so you pay for maintaining a big fleet. This will force you to expand if you want a large number of ships.
This is basically the end solution that was arrived at in prereleases U and V, only instead of tying it to individual ships (complicated, CPU-costly), it's tied to the energy reactors themselves. But yes, I think this will really help to make for a more balanced, reasonable flow upwards.
OR force the player to take over a system / planet in order to gain the research from it...
This is a very intriguiing idea. I very much like knowledge raids, but I could make it so that you can only get 50% of the knowledge off of planets that the AI controls. What does everybody else think about that? I think that could be really effective without completely ruining knowledge raids.
I am also for having research be able to increase the ship cap on ships beyond unlocking them.... Instead of starting with 350 mark 2 cruisers for 3000 knowledge or whatever it is maybe it should cost 500 for 30 of them... then 500 more for 60 total, then 500 more for 90 total... this would give players a little more flexibility at the start as well... and the numbers could increase to beyond what is currently available. if I want a fleet of 1000 mark 3 cruisers with 20 of every other ship I should be able to do it ;-)
The ship caps are the way they are in order to prevent players from just spamming their favorite unit, which is what happens in most RTS games. That's actually been praised by a number of reviewers for being an innovative thing that really increases the strategic options -- having to use your older ships as well as your bigger and better ones is really unique and adds a lot (like having pawns in Chess in addition to the other pieces, rather than just starting with pawns and eventually having an army of queens, which would be strategically moribund).
But, all that said, some logistics hubs or similar are planned for an expansion to allow players to turn knowledge into increased ship caps for their favorite ships. That's definitely something for an expansion, because it will require testing and balancing (and it's a pretty huge gameplay addition in general), but I think there's still a fair bit of support for something like this. It's just going to be an augment, though, not something that is intended to just let you roam the galaxy with massive cruiser fleets that are impervious to all else.