In a few moments I"ll be previewing v1.01 http://www.twitch.tv/stardock
You mentioned that you will likely add a shield regen unit to Substrate even though you'd prefer not to as it will make them more similar to PHC.
I think a very reasonable alternative to that would be a T2 bubble shield unit. It is a different way to preserve units shields a little longer, or give them more time to slowly recharge under fire. It would fulfil the function you want, would be a crowd pleaser, and all while allowing the play style of Substrate to further diverge from that of the PHC instead of doing the opposite.
I'd make it fairly expensive, probably a high Radioactive cost. The Substrate can take that as they can upgrade their eco. a lot more than PHC.