By doing this though, all you've really done is re-invent troop transports. I'm not going to put armies in a ship that's going to go into a fleet combat because they won't be as good as real combat ships, so I'll just design a "troop transport destroyer" and a "fleet destroyer", and we're back to separate troop transports.
Better to just have a proper army-building interface and an army capacity stat that's increased by army buildings. That way armies could be built as easily as fleets can, and would no longer be effectively limitless in size.
But would still have to be microed separately, increasing the interface fiddle that a player needs to deal with and causing the AI the tragic weakness that it can never effectively protect them and always loses them making it even crapper at war.
Making them part of ships would make the game better, better for players and better for the AI because it can't screw it up as bad. Whether it satisfies your craving for verisimilitude or not.
A bit later in the game the Focused Arc emitter + 4xCloud Lightning gave it good competition, but Cloud Lightning got a stealth nerf so I don't think it matches up as well any more. I still tend to use that one though because I only have to worry about energy weapon improvements.
Only at frankly unrealistic levels of repeatable technologies, by which time the game is almost certainly long since over. AE+CL can be a specific counter to the Contingency because they're shield/armour heavy but is generally worse otherwise.