I know what you mean,
for example in the game MOH:AA
(Medal Of Honor)
they where able to create a supermod that tottally change the game
it turned into a Arcade Flight simulator that was really fun to play
it was very amusing to test the mod.
the goals was simple bomb the enemy bases. you had fighters and bombers.
the airfield where protected by AI Flak guns that really packed a punch when you came in range.
unfortuantly the damage models where based on hitpoints so it was just the matter of the amount of bullets you nailed into the enemy. but like in FPS the hitpoints varied on the locations (Cockpit and engines where critical locations to be hit on)
like in known in SH3 the limitations are on Player controlled Submarine only.
too bad thought but thats how the game has been made.
becaus if it was posible to mod the game to add new controlable ships (BBs/DDs)
and even planes that would really be a impact on the game itself. just imagine in Multiplayer that you blast eachother to pieces with Nelsons and Hyper Heavy cruisers