I have a few thoughts about this topic, so I'll start with how I design ships. I do usually like building larger hulled ships, but I've found that small/tiny ships can be very useful in a 'supported defense' setup. If you intend for your fighters to just operate in the vicinity of your military bases, you can pass on giving them any kind of sensors, support mods, and possibly any engines, as they will always be within the 'shadow' of your military base. Here, each ship gets the bonuses your base provides, and with a potential for +16 to each attack type per ship, the more hulls you can manage, the better. Add in the benefit of having a subspace wake/inverse tractor beam, and you really don't need weapons on these short range fighters, letting you pack in a lot of weapons/armor on your 'fighters'. Then, just combine them into the largest fleets your logistics will allow and have fun. (Mind you, I haven't fully tested this, but it seems quite feasible.) Obviously, in areas where I don't intend to have the support of large, well-equipped military starbases, I will tend towards larger hulls, which are more robust when operating independently.
Secondly, I've been thinking about this for some time now, and I think that one major reason we don't see more variety in people's selection of hull sizes is that there is no consideration of accuracy in combat. The attack and defense rolls work the same regardless of whether the target ship is tiny or huge. Obviously, introducing an entirely new variable into combat is not really desirable at this point, but there is a way to simulate this factor in combat. By applying a defense modifier based on hull type, you could simulate the fact that smaller ships are harder to hit and less likely to take large damage, and at the same time simulate that larger ships need more defensive components to protect their larger bulk.
Implementing such a modifier might be a good idea for a minor mod, but I really lack the programming ability to make this happen. Maybe it already has and I'm just not aware of this, or maybe the programming doesn't support such an option of adding a modifier based on hull size. Still, if anyone's interested in the idea, I'd be glad to post my thoughts on such a thing.