There are a couple ideas I'm thinking about, that I imagine aren't too difficult to implement and which I think would add a lot to the game were they included. I think these are important concepts and, once I get a bit more time on my hands, they are both things I would be interested in implementing myself (if they're liked ideas and nobody beats me to it at least). They are one-ship fleets and "critical ships" (not sure on the name of that second one). Apologies if any of these are already in the game, though as far as I know none of these are.
One thing that I think could spice up the game a lot is the existence of certain very powerful ships, with the consequence of there being no fleet to support it. The big one that immediately strikes me as a good candidate for this is the Exodian Blade. It doesn't have an army - it is the army. Other ships that I can think of that strike me as good ideas for this would be certain very powerful golems, raid ships with cloaking and fast movement that can strike into AI territory without having to worry about leaving other ships behind, and perhaps a sort of "Mobile Fortress" - a structure that creeps along at a snail's pace but serves as an extremely powerful structure meant for defending chokepoints. All of these would be ships that are plenty powerful on their own, not really needing a fleet, but able to be reinforced with fleets if they're around anywhere. I'm aware that there's already some of this in the game, but I think it's an idea that could be fleshed out some.
The other idea I am interested in, and one with which there is some crossover, is the idea of a Critical Fleet. I started thinking about this when Puffin commented that losing a fleet was often but a temporary harm, since it would be rebuilt in time. I don't have any issues with that - in Classic and pre-fleets, you could replace nearly anything with time. Making every fleet centerpiece lost permanently would be analogous to only ever being able to build five of a kind of starship - not having five at once, only five, and if you lose them you're not allowed to build more.
Emphasis on "nearly", however. One thing that I think would be very interesting is having certain important or powerful fleets not be recoverable if lost. These are ships you could use sparingly, only when you really really need a boost, or perhaps something you build your entire army to support and protect. Again, the Exodian Blade and more powerful Golems seem like good candidates for this sort of thing. Arguably, mobile fabricators and Arks could fall into this as well (though losing an Ark permanently is very, very harsh...). There could also be a fleet like the Advanced Factory, that marks up all allied ships on its planet or of a particular fleet, but if you fail to protect it you lose it for the rest of the game. I would say that anything sufficiently "alien" could count as this - something where it makes story sense that the human remnants wouldn't know how to rebuild it if it were destroyed completely. This would help keep the game in line with Classic, in which most fleet ships and starships could be rebuilt at no cost other than metal and time but certain structures could be lost forever if you weren't careful.
Neither of these seem (to me, at least) like they'd be very difficult to implement. The former is simply a hero unit that has no other ships, and I'd be surprised if there isn't a bool for "destroys-to-remains" that could be toggled to cause permanent loss. (I suspect the Factory might be tough but I'm not sure). What do you all think? Are these interesting ideas that would improve the game, or are critical ships and one-ship fleets better left on the cutting room floor?