It's hard to say what we'll see in Utopia since I don't think it's been discussed. I think that large, limited ships are a good idea because they can also cut down the number of ships on the board at the end game, thus improving performance. I know that's not the most exciting use for them, but imagine there were no ship classes. A 100k fleet would be even more ridiculous.
I'd also like to see some of that The Fleet for AlphaMod does where it allows you to unlock some more specialized sections and roles. Rather than throwing in a bunch of classes of ships like NSC, you just diversify the ones you have a bit more. As for a Titan though, you could balance them the same way the megastructures are. If I remember correctly, most eat up a system. So, if you had to consume a mineral-producing planet per ship, you'd be limited both to the number that can be created and to removing a resource generating planet from your systems.