3. Starbases need the ability to inhibit phase jumps. This would increase their strategic value in uncolonizable systems tenfold.
While you are right about their value in uncolonizable systems, that would make phase inhibitors worthless in other systems that host a starbase except as a backup. There seems to have been a deliberate design decision to make sure that starbases do not replace the existing tactical structures but supplement them, and that any module that mimics a defensive structure should provide about 10 tactical points worth (see hangars, vasari phase gate).
It might make sense for one faction to have it available as a faction specific module, but all those slots are already filled and with things relating more to the core phiolosophies of the factions.
I have one other thought on defensive emplacements. Given their available upgrades, I feel that a more modular approach would be a better way to go. In other words, give every turret a fixed number of hardpoints, and allow the player to choose how many and what type of weapon system he would like to install.
More micromanagement and harder to balance. While I'd probably find it fun if we could individually configure every single weapon hardpoint, I know that I, and others, would be working overtime to come up with degenerate solutions depending on just what we were facing, and that we'd find them. It leads to the usual issues of "if I allow you to build as many of X, Y, Z up to the sum being N, and somebody makes N X's and it turns out to be too effective, how do I change this without making other number of X's (say N/2 X') ineffective?" Cue diminishing returns, penalties for overstacking &etc. Given the focus of this SoaSE, adhering to the KISS principle where starbase construction, management, and maintainance is concernced is probably the best solution.
All the reasearch requirements would stay the same, but at the same time you could essentially make three different types of turrets depending on need. At this point in time I feel that the platforms are a "do everything ok but nothing great" type of structure.
In other words, a platform that's pretty capable of handling most things that are thrown at it rather than having glaring weaknesses against some types of attacks* - with the exception of the dedicated anti-structure vessels.**
* Such as lone heroes attacking critical weak spots without being hit because the defenses aren't trained to deal with their skill at maneuvering.
** And huge numbers of strikecraft, greater than the number you may, or may not, have chosen to put on the starbase. But then, if somebody attacks a starbase with huge numbers of strikecraft and the defender doesn't bring up anti strikecraft buildings, flak, or their own strikecraft, the starbase doesn't deserve to live.