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.
It would also help having sort of "governor" settings, to group different types of starbases together so you can set a default upgrade stance, versus others that might prioritize upgrades more or less. Not to mention global settings of any type, since disabling the auto-upgrade stance on each new starbase gets a bit old.
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