WARNING: POTENTIAL LONG POST AHEAD
Here is how I think the balance for armour vs shields would work, this is just my opinion, if you have any contributions or suggestions they are more than welcome.
Fighters and Bombers: Main defense is through shielding to avoid slowing the ship down. Once the shields are destroyed the fighters will be easy pickings for even the lightest of weapons, meaning one shot kill with most weapons once the shields fall.
Frigates and Destroyers: These ships will be large enough to moutn a certain degree of heavy armour with less worry about manueverability than the fighters and bombers. However, once the shields are down a squadron (5-10) of fighters should be enough to take it out with little difficulty.
Light Cruisers: These ships will mount a significant amount of shielding and armour. Their shields will regenerate quickly making it very difficult for fighters to do any significant damage whilst they are up. Once shields are down the armour is sufficient to withstand a couple of shots from battleships and dreadnoughts before destruction. However, a bomber equipped with powerful explosives or missiles could deal catastrophic damage with appropriate fighter escort.
Medium Cruisers: Similiar to light cruisers, except that fighters are now completely worthless against the shields, with even dozens to hundreds of fighters hardly making an impact on the shields. The armour will start to become a significant defense, meaning that frigates are only a moderate threat, even without shields.
Heavy Cruisers: Because their armaments are becoming more powerful, these ships will be almost impossible to deal more than minor damage to when using destroyers and below, even when shields are down. Their shields are still strong, but no match for the amount of firepower that can be utilised by a battleship or dreadnought.
Battleships: These huge ships (500m-1km) are very slow, but in return they get amazingly strong armour, which means that an unshielded battleship is still an enormously dangerous threat. Even insane swarms of fighters (around a hundred thousand) just cannot do anything because their guns cannot help. Battleship shields are no longer the main defense, because the regenerative ability of shields is not effective when faced with the huge broadside firepower of opposing capital ships.
Dreadnoughts: These ships are even larger (1km-2km) and therefore even slower than the battleship. Shields are almost useless now, but this is compensated for by the insane thickness of armour these ships carry. Nothing less than heavy cruisers will so much as slow down these behemoths.
Mothership/Flagship: These insane ships (2km-5km) are so insanely powerful and slow that only the largest alliances and governments would even dream of deploying one. These ships are the pride of the alliance or government they belong to. Their speed is almost non-existent, but it hardly matters. Many of these ships will not even mount shields, choosing instead to mount armour hundreds of metres thick (yes, hundreds of metres thick) which means that nothing less than a fleet of opposing battleships and dreadnoughts will make this ship flinch. Deploying fighters is too stupid for words, even tens of millions will simply have no effect at all, even if allowed to fire unimpeded.
Sorry for the long post guys: the TL; DR version is this: For smaller ships up to cruiser shields are good so that they can remain manueverable, whilst above that size class, when speed is less of a concern, armour becomes the go-to defense.