Thus far in Sins, giving your capitalships and titans an advantage on the battlefield has meant only one thing: let them blow stuff up for experience and levels. While that's probably superior to them needing to be purchased, thus giving the players with superior economies a huge advantage, it may seem silly that you can't even purchase a little extra armor for your prized level 10 Marza Dreadnaught. With Enhanced 4X 1.5, that's going to change.
The Upgrade System
Almost all civilian structures in E4X have been given alternate affects on your planets besides their intended purpose. Research labs can help construct bomb resistant buildings, refineries can boost your trade income by increasing the amount of goods available, etc.. But factories have thus far only been about producing ships. Now Capitalship, and Titan factories will be able to provide various, race specific upgrades to the ships they produce, for a small fee of course (though a few maybe free after some research). These will range from simple stat bonuses, like that armor increase, to complex functions that almost work like all new abilities, like an emergency phase drive on TEC capitalships that will allow them to escape from phase jump inhibitors every so often. Titans will also have one upgrade that is unique to the subfaction, not just your race, and all titans will gain an upgrade to make them deal with bomber swarms better, so if you can't take them out if a few passes you may find all of your squadrons shot out of the sky.
The upgrades will be unlocked via a tier 5 military research, so these won't come into affect until late game. In addition, both these factories and the units they are upgrading will be disabled until the upgrade is complete, so don't try to upgrade in a battlezone. Heroes will be able to receive capitalship upgrades, and while you can't upgrade frigates, frigate factories will gain an additional function as emergency repair platforms.
While I've mostly decided on what upgrades I'll include, feel free to leave ideas in the request forum.