But who said that this has to be true?
The concept of mixed fleets might be true here on our planet, but that has more to do with a lack of technology: armor is just not viable anymore and propulsion is lacking. That's the only reason why smaller ships are used (as they punch well above their weight class) and why aircraft carriers are as slow as they are. If we had armor that could only be penetrated by big enough guns, if big ships could move as fast as small ones, I assure you we would see a strong trend towards big ships. Or - in terms of Stellaris - if a Corvette was always ten times faster and always had enough firepower to kill any battleship, I'm confident that everyone would avoid building those in favor of Corvettes.
That's why battleships in Stellaris are superior to everything else, because both aforementioned problems are eventually solved by technology: shield/armor tech keeps up with weapon tech (which makes bigger always better than smaller) and propulsion tech allows for moving big ships at a fast enough rate to keep up with smaller ships.
Solving long-standing issues like those is reflected ingame by gaining certain tech (meaning Gateways, endgame Thrusters and also targeting computers), which causes all three ingame advantages of smaller ships - speed, evasion and piracy-suppression - to lose their edge. That is the very definition of the word obsolete: becoming out of date and being replaced by something better. That's why it is comparable to starbases, as it is a very straightforward approach by offering upgrades without drawbacks (aside from the resource and time costs of course).
I understand that from a realistic viewpoint one could say that troops/ships/armies/navies always needed to be diverse and the same should go for warfare in space, but arguing for realism in a galaxy that has giant dragons and undead is quite a moot point. It is believable enough that tech solves problems and reduces micromanagement, so good enough for me I guess.
And funnily enough, a bit of the dreaded realism to the whole question of speed would even invalidate the very idea of smaller ships being always faster than bigger ones, as the whole thing is just a matter of propulsion and mass. If the ratio of both remains the same, even a Juggernaut might become as fast as a Corvette.
Anyways, the game doesn't forbid mixed fleets, you may use them as much as you like. It may give you a bit of a disadvantage in competetive multiplayer, but then again, so do other things as well, like choosing the 'wrong' Ascension, traits or origin.
I see no need to change a working system. There are a few things that are broken in this game, but this here isn't one of them.