Make shields REALLY do some considerable protection/handicapp against their strength/weakness, respectively.
Like Graviton shields block 3/4 or 1/2 of Laser, photon and pulse, but do the opposite against particle and plasma, not just 1/100 improvement...
OR
give armor the same capabilites as shields to block specific damage(s). Maybe a Zero-Point armor that works like Molecular shields, but an armor-hardpoint.
Would help diversify weaponry and strategy even further.