Stargates should consume energy to transport ships based on the distance traveled and the mass of the ship, so a huge corporation displacing their whole fleet would have to dish out some serious dough, while a small band of friends could still travel through the universe fairly fast and cheap.
Additionally to cost, there could be a queue system at stargates with different lanes, so that ships with smaller mass get processed faster than larger ships.
And lastly the construction of stargates could require rare resources that the devs can control the available amount of, so that only few stargates will ever be built and thus only connect a few main routes.
Another idea could be one-way jump beacons. You drop a beacon somewhere, and can later establish a wormhole to that point. This would mean that only returning would be fast (but maybe still costly, depending on the mass of the ship and the jump distance), but to head out into an unknown region of space for the first time would take a while. Could also introduce an interesting mechanic in that other players could try to find other people's jump beacons, and either destroy them or set up an ambush at that location.
Also you can't say absolutely that large ships can accelerate faster than small ships, or that they can reach higher speeds. The former only depends on the relation of their thruster output to ship mass and the latter on the relation between fuel carried and ship mass. It is hard to say if a larger ship would have a larger fuel tank compared to it's relative mass, because everything else also has to scale up (you need more gun mounts for defense, more mass dedicated to structural integrity, a larger shield generator, maybe even emergency pods and scout ships, etc.).