Would it be possible to change them to ruined buildings (ie: no roof) that get garrisoned?
Some players argue that they are unfluffy (dome void shields have been mentioned in Black Library novels but fine, whatever) and look silly.
Relic argues that the directional cover of DOW2/COH doesn't work well for large armies, and it's important for it to be visually clear when units are in cover.
So just changing the appearance of them to something more palatable to the fans might be a good compromise.
It surely wouldn't take a lot of time/money to model - it's just a bit of building ruins not a fully animated unit. You could even still have the health bar or a cover icon appear above the cover. The current bubble shields are already halfway there: they're basically a set of short walls with the energy dome over the top. Remove the energy dome and add more walls.
The actual function / mechanic of cover would remain the same. The change would only be visual/cosmetic, but perhaps improve the "feel".
It already seems like it can be difficult to see units in cover due to the visual shield effect, so this compromise might even help in that regard.