Europa Universallis has a maximum support limit on each space exceed it causes your forces to weaken through attrition. Also army moral is a key combat stat and much larger army can be defeated if its moral is low from constant fighting. You could have something large fleets exeeding your supply range and capacity could gradually weaken. damage, and max hp, and shields might decrease every turn, they might run out of missiles, or ammunition.
You could have a logistics stat which determines the max fleet sizes or the maximum number of ships you can own.
Planets and colonies might be highly vulnerable unless defended ala Risk. Forcing you to leave ships behind to defend or have newly conquered territory taken away very easily as you front expands.
The speed of the fleet might be based on its size. 1 small ship moves 10 parsec a turn. 10 large ships move 1 parsec a turn.
Scorched earth anti colony weapons are devastatingly effective. 1 fast attack ship making it to a colony is enough to destroy it.
MOO2 had telepathic control which was my main tactic. A cruiser or bigger can instantly convert a planet to your side once its defences are destroyed.
Privateers/partial knowledge raiding/destroying can be done as a stealth action. If you have a small and powerful enough force an enemy colony can be raided or destroyed with out the enemy knowing who attacked them. Based on distance from their capital, the size of the attack force, and number of turns spent attacking.