If you are doing a TC, then you could set all capital ships to have enormous armour but only the same level of shields as smaller ships. Smaller ships, on the other hand, would have very little armour.
If you then set most of your weapons to have high damage against armour but low damage against shields, you would effectively create a two tier system which gave small ships advantages against certain classes of weapon.
Of course, you could then have some critical hits weapons which pass through shields - deadly against small ships but not so effective against capital ships.
One of the big problems of EVx is that nobody has ever bothered to define how shields, hyperdrive etc actually work, so cool effects of this nature would go rather unnoticed. However, in your universe you can define them anyway you want.
Some interesting examples: Frank Herbert's Dune has shields which will not permit fast objects to pass through, but allow slow objects
Asimov's early work (eg, Black Friar of the Flame in the Early Asimov) has ships where the shield has to be momentarily dropped in order to fire. You would have to think for a moment about how to implement that.
Unfortunately, most people seem to have been brought up on Star Trek, which has one of the most uninspiring approaches to shields (although eminently suitable for the Star Trek games which were Elite's predecessors).
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