This is exactly what leads to PvP consisting of only titans. Larger ships give more flexibility with design, yes, but they shouldn't be ABSOLUTELY INVINCIBLE to every other ship smaller than it. I'm not saying that fighters should be able to dunk capital ships but capitals shouldn't be the end-all of combat.
edit: furthermore, just because your ship is bigger/more expensive doesn't mean it should automatically be "better". outcome of combat should be reliant on player skill just as much as it should ship design.
example: My '03 Ford F150 can carry more furniture than your '14 Camaro. Does that mean it's better? No.
example 2: The IJN Yamato was the largest, most powerful Battleship to ever sail the seas. Every time she saw combat she was beaten back by TBM Avenger fighter bombers of the US Navy. She was eventually sunk by these type of bombers in 1945, during Operation Ten-Go. Was the Yamato more expensive than the TBM Avenger, or even the carriers that launched them? Which one was more effective in combat? (to clarify, the Yamato had a greater displacement/mass than any US Carrier of the time)