Okay this is a thought I had.  How about using the level system of cap ships for starbases.  Now before you go shooting that down saying it's already been thought of just read this. haha

Basically, you build the framework of the starbase taking about the amount of time it does now.  You can't upgrade anything on it right when you build it.  Then the base gradually gains exp until it levels up.  Then it gets limited weapons and some more hp.  Keep doing this adding to the sp/hp until you get the full starbase construction complete maybe around lvl 5 or so.  Then you can start adding your upgrades to it.

Then of course there'd still need to be the basic buffs to starbases that everyone wants because this increase in build time.  No one would want to invest all that time just to get the starbases as they are in the game now.

Though this method would eliminate the use of the starbase in offensive capacities.

There's also the fact that with this system when an enemy scouts and sees that you're building a 'base, they'd be able to react and try to destroy it before they "witness the firepower of this fully armed and operational battle station!"

Okay, have at it!