Yep definetly B5 for watching it. For how to chuck it into the story I do like the FreeSpace2 style. There's some line in the editing manual along the lines of making the cap ship combat roughly even with the fighters/bombers the deciding factor. So one decent bombing run can tip the balance, one 'suicide king' turret run can knock effectively take a cap ship out of the battle.
As for variable ship size, hmmm... Well you wouldn't need full DNs everywhere, just in your main fleet(s). There would be smaller ships for anti-pirate duty, convoy escort, etc. Plus say (battle)cruisers which are faster but less guns/armour. Dedicated anti-fighter escort vessels as well maybe, because your aren't going to waste space on a ship of the line with too much anti-fighter weaponry are you.
For ships of the line, if you want to use the Royal Navy system then Dreadnought is big primary gun only while Battleships have primaries and smaller secondaries for taking out yappy things.
Mind you, when (if

) I carry on my stab I do plan to use most of the above ideas..
