Quote Originally Posted by Musashi
Personally my preferred solution is to put double their shield value into defense skill. This counteracts the negative value, and gives them the melee advantage that they would normally gain from the shield, leaves them with the shield value against missile fire, and basically doesn't overpower them at all in normal play. It makes them overpowered in autocalc, but I never autocalc a battle so it's no big deal to me.
This is what I am also using, though I also upped the defense skill of the units without shield to compensate for autocalc and AI building priorities. So far the battles have been playing out nicely with these changes.