[Paladin]

Btw, there is an "Upgrade Facilitites" option in the construction queues main window (F7), and in a given planet's constr.Q...
Using the later will prove tiresome, but the global setting will try to upgrade ALL of the facilities at once (real expensive...)

On the other hand, I don't think that auto-upgrading ships would be a good idea, since it costs so much to do so, and your ship needs to be at a spaceyard to do so (not a problem with "Engineer class" cruisers ;-)
Then, auto-upgrading really is difficult to decide wich ship to upgrade to, since there are most certainly more than one available model for each ship size...
(What would be needed is a way to retrofit a fleet, all the ships of a certain size regardless of their different model, and to be able to SEE THE CLASS in the scrap-retrofit-mothball window...

Aside from that, everything is looking good (altough Master computers III are expensive, ouch! )