First, I think the new starbase management tool is a substantial improvement.  Kudo's!  What I would like to see is a control on each of the installed modules that further defines what installed modules are auto upgrade-able.

As an example, I may have an econ starbase supporting a couple specialized research planets.  I want the labs to auto upgrade.  However, I may have initially installed a starbase factory to boost up manufacturing while building out the planets but i don't want to auto upgrade the manufacturing module.  Similarly, I may have thrown a level 1 perimeter scanner on a starbase, but I don't want to auto upgrade the scanner; just the main module(s), be it research, manufacturing or whatever.

Adding this additional control would allow me to use the auto upgrade much more frequently.