[Suicide Junkie]

Realistically, how is that supposed to work?
The plot isn't going to change just because you upgrade your ship...

I do believe there is room for more difficult random missions, but at some point it gets silly.
The Abbidon mercenary missions that put you up against Battleships with Cruiser escorts should be plenty challenging (and they are in the P&N mod)

Perhaps you are looking for more disadvantages on the large ships...
- easier to hit
- much slower (IE battleships can't run if they get into trouble, and can't get to where they're needed swiftly)
Perhaps they need to have less of a shield/armor advantage over other ships.