I think the idea of making initial star bases relatively cheap is counter intuitive. I mean, the things are huge(well, I think they should be still larger, dwarfing capships, and second only to the planet). They should be a high development cost in credits, high in metal, and med-high in crystal. This would prevent any spamming until the late game. You would likely only be able to construct a handful at key points. Also, constructing them should be slow, so they need to be protected by an escort fleet. Upgrades, on the other hand, are modular in nature and should be researched and installed fairly quickly, for an average(tier 3-5 tech)cost. They should be able to be removed, with a fairly long timer so that a trade and support starbase can't be instantly retrofitted into a tank starbase whenever it gets attacked.
I like the idea of the constructor(which should be a unique ship for all races, and much bigger) being built at the cap ship factory.
TEC mines should be reduced in cost, not use a tactical slot, and have cap of, say, 200 per grav well. In addition to that, every 45-50 or so mines should have an impact on trade/refineries, due to the increased navigational hazards. So maxing out your mines would seriously hamper trade, while placely some strategically would have little to no effect. Planets without trade ports or refineries(unlikely) would be unaffected but still have a cap on the total number of mines
Vasari and Advent mine ships should have a set number of mines each can lay(possibly increasing with research). The ship would then be able to lay more until the originals were destroyed. So, if you want to spam mines, you must use the majority of your fleet supply to build a lot of ships that are easily countered. And, the ship woould be useless if the enemy manged to bypass the minefield.