Make starbases use cap ship slots.
It is rare that players will use up all their capital ship slots in the game. More often than not frigates are better for cost, and eventually the fleet will fill up with only a modest number of caps. This leaves over half of the cap ship limit unused and unloved.
However, balancing starbases is tricky as is. If each system is allowed the same thing, then starbases have to be balanced as a moderate defensive unit. They can't be fleet crushing wonders AND litter your entire empire at the same time. They certainly can't do it for cheap, or players could never break the defensive lines for cost.
Starbases are massive structures. They're bigger than cap ships, have larger crews, and more advanced weaponry. Make them use up a cap ship slot to produce. This way, the structure made to turn the defensive tide has a hard limit. They can't just be spammed at every grav well, players have to decide where is the most important to defend.
Without the guarantee of having starbases everywhere, the individual structure can be enhanced to be cheaper, stronger, and deadlier at every turn. Or, it may simply allow 2 of them in a single grav well, if you can chance your other planets getting none.
It also means that the number of starbases is controlled by the tech curves in the game, instead of going directly from zero to everywhere.