I really like Hexx's idea, but a couple of questions remain for me.
#1 If you include Command variants you still have some of the best PvP ships in the mix. Take the Novahawk, the Fed CB, the L-CWLP for example. Perhaps command variants should be eliminated from the "line-ship" category. Of course will "aces" be willing to fly "line ships" if they aren't among the best for PvP or will they go with the better ships trying to drive folkes from hexes instead of going for PvP points? I'm guessing not many would go for the line ships if it put them at a significant PvP disavantage with the disengagement rule in effect.
If you really want to encourage the line ships what needs to be done is to make only "line ships" force a disengagement as well, or perhaps make specialty ships only force 1/2 as long a penalty. With the current game philosophy of forming "hunter/killer" teams to win control of hexes I really don't see the "aces" as willing to give up their specialty for their whole team for fear of being chased out of the area just on the chance they might earn a PvP point or two.
I see alot of negetives to this approach of only "line ships" forcing disengagement as well.
#2 some race's "line-ships" are more capable of getting a kill than other race's line ships. Crunch power, fighters, drones, power curb, etc. all come into play. Defining what exactly is a "line ship" is a very tricky business, for example are "heavy War destroyers "line ships"? By late era most ships just simply don't likely qualify for one reason or another. Not sure there is anyway around this as it also applies to specialty ships and is likely just a racial feature.
What would I do?
Likely go with Hexes rule for most of the map with the addition of only "line ships" being able to force disengagement. However,once you get to withinin 1 hex of a base or planet have all ships able to force disengagement and all ships kills count. I don't think the vets will short-change their asenals so close to a VC area in the name of PvP points anyhow, and the vets need some good fights with high stakes. This will keep the really hot zones dangerous but allow for more new player friendly areas for large parts of the map.
I really like some aspects of Hexx's system. Under it there is no reason to not offer mercy to a new player if you are flying a specialty ship, he/she isn't worth any points. It might provide opportunities for them to learn better power management as hex pointed out while flying the "line ships", and it might encourage vets to fly line ships so that a newer player in a specialty ship can offer a more challanging fight to them and also gain more PvP experience to the newer player.