Why don't we just come up with a reason for us all to be limited more?
We don't need millions upon millions of ships (The logistics of fielding these would be pretty crippling anyway)
Some quick fleet statistics from various sci-fi
Covenant (Halo): Contain a large portion of the Milky way (Probably about 1/100th). Fields Several Thousands ships, probably just under the 10,000 mark. Largest fleet fielded has a bit over 500 ships, the fleet tasked with the destruction of the Fortress world of Reach, Even if we times this by 100 for controlling the entire milky way we have just about 1 million
Imperials (Star Wars, Palpatines Empire): Controls pretty much the entire Star Wars Galaxy, at it's peak has Millions of Ships (Though this includes transports) The largest fleets fielded (If we are to trust the movies and games and not the weird extended universe which would take me 50 years to read through) seems to be several thousand large at a time
Imperial Navy (W40K): Controls Millions if not Billions of Worlds. No clear number is given, but a sector is given a battlefleet of about 200 ships, and given the amount of Sectors we're probably looking at the 20 mil mark (From the most blown out of proportion empire in the history of Sci Fi. Average Battlefleet is the aforehere mentioned 200 ships, with the largest battlefleets having several thousand and being tasked with 'Exterminatus'
Void of the Stars: Average Warfleet appears to be in the Hundreds of Thousands range, with the largest fleet being fielded probably had over half a million if that fleet of the AIF that engaged the Goa'uld was supposed to be the largest fleet ever seen in the Milky Way. A quick and basic calculation (Thus not entirely accurate) concludes that the AIF alone has 100000000000 (100 billion)
Why the hell do we need navies of 100 billion to throw at each other? Aren't thousands (10's of thousands if you want to push it) enough? These things aren't cheap to build or operate, we have ships that are many, many km long in this. You need immense amounts of energy to break orbit then move them to light speed, supplying billions of these is economy suicide. What about the logistics of providing for the quadrillions of crewmembers during war time?
Also, from a gameplay stand point it's gotten stupid. We have so many ships our strategies are basically to line up our fleets line old Colonial regiments, form firing lines and trade fire until one fleet burns, because any attempts to perform tactics with such large numbers would just result in chaos.
Smaller fleets, smaller armies, more detailed and strategic fights. Right now it's "I THROW THOUSANDS AT YOU" "WELL I THROW TENS OF THOUSANDS" "I USE UBER WEAPON!" "I CALL IN MORE HUNDREDS OF THOUSANDS" "I SHOOT AT YOURS" "SOME DIE BUT THERE ARE STILL MANY LEFT, I SHOOT AT YOURS" "SOME DIE BUT WE HAVE LOADS LEFT, OPEN FIRE!" and so on