One thing that you have to keep in mind with the number of hull designs is the battle screen. If you allow more designs, then you have to deal with more stacks potentially in a battle. Too many designs would mean that some ships wouldn't fit into the back row of the screen, and would start out closer to the planet (unless you limited the number of hulls that could group together into a fleet).
It could also lead to cheesy tactics like bringing 10 identical ships knowing that missile bases can only target one per turn, allowing the rest to reach the planet (even if a single missile volley would have been enough to kill all 10 ships stacked together).
I did like the concept of limiting the number of different designs per hull type based on race. I think the AI in MOO already does this to an extent, since different races prefer different sizes, though it would be interesting to apply some limits to human players as well. Rather than 12 designs though, I might go more along the lines of
Alkari: 4 small, 2 medium, 2 large, 0 Huge
Meklar: 1 small, 1 medium, 3 large, 3 huge
but have the total design cap remain at 6. The Alkari would be able to have 2,2,2; or 4,1,1; or 3,2,1; etc. They would still be relying mostly on smalls though.
One of the issues here is that you can't give a race 0 smalls or larges, because everyone needs scouts and colony ships.
One possibility of a remake would be to have 6 military design slots, and have scouts and colony ships designed automatically (perhaps allowing their engines to auto-upgrade when new ones are discovered so older scouts never need to be retired). LR colonies would still need to be designed using one of the 6 hulls, but they are usually used for a very short period during the game. You could also code the scouts and colony ships to never enter combat, thus no scout blockades. I'd also like to see scouts that encounter defended enemy systems to at least update the map with the name of the system, and the flag of ownership. I never liked having to remember which occupied planets my scouts had been to, and which was which. No need to treat them as explored colonies, where I can see the pop and base count, but more like the colonies you learn about through contacting a race.
I feel like a remake would be great if it stayed as close as possible to the original, and any new features were optional.
There would be some things to improve about the AI though. One would be giving it a better criteria for scrapping designs. It's painful to see the Alkari flying around with several thousand laser fighters trying to shoot down ships with class 8 shields and particle beams.
It's tough to write the AI so it can't be abused; if they AI were to monitor the enemy tech levels, and scrap ships once enemy shield levels exceeded their weapon strength, the player could research high level FF, get the AI to scrap their fleets, then pummel them with ships with no shielding. Maybe the AI could "cheat" by knowing what the players hull designs and missile base techs are. Then it could scrap ships that would be ineffective vs. current base shielding and ship designs (though a minimum number of ships would need to be built of a particular design before the AI considered them, to prevent players from just putting up an empty design to fool with the AI).