There is a need, to power the two battleship slots, which is why its called a battlecruiser.. Part battleship, part cruiser.
I semi agree with the capships in guard systems, however.. this won't solve the problem with the people who already have capital ships, and players will just do missions until they are neutral to the guard. And can do it when owning faction of said system is away.
Bombers are just as bad as capships, imo.. i've seen them abused too much, example: Bringing a lone bomber to a fighter fight with no escorts, or no capships to destroy. A little nerf is in need here, bombers should be depending on fighter craft to protect them, Not running around gung-ho blasting away supernovas at fighters.
As for trade routes, you will always have a oorp trade route, unless each and every possible trade route is calculated, and all possible ways/shortcuts to get there are found out and the ones that are "oorp" are either removed, or the route itself is changed. Some of these routes we already know of, I think the artifact run, the cardi run, and the diamond run are the worst of them all. Hopefully something can be done..
And i also agree with the train cd's, while the current guard npc's are still powerful, they could use a boost in power, by adding a train cd.. Will make power traders/smugglers think twice before entering a guard system:P