IpityU - There might be an Artifact that increases shields, but I don't have one in my Vault so I can't be positive.
Don't know if you know about these already, but here are some things you can do to improve shields for all ships (including commander and prototype) automatically -
1) Building Institution of War (Orbital)) gives all ships +5% shield strength
2) Building the "Ironside Resonance Emitter" adds 10% shield strength (needs 2 Gigamass to build)
There are probably more, but these are the ones showing up on my ships currently.
This one is pretty basic, but again it impacts all ships - researching various techs on the "Defense" branch will yield various shield improvements