Would you mind give some details about what is wrong in the Destroyer? As a guess I would say it's something with the medium mount, and the flight deck, but not sure
Saying "what is wrong" is a bit iffy because with the concept and general hull design, everything's fine. But the kitbash isn't very well painted. There's a ton more room for smoothing and cleaning up of armour sections, and there are some sharp angles where (for instance) the hangar bay and the medium hardpoint meet the front part of the hull... Also the bit alongside the bridge where the reactor is, looks like it should be a white to match the bridge, rather than the high-tech armour blue. And the very front small hardpoint looks very alone, almost like it was stuck there as an afterthought - maybe try shifting it back a bit to integrate it into the rest of the hull a bit more smoothly?
Oh, and it's also incredibly obvious where the bridge comes from. Believe me, I made a similar sort of 'bash and one of the problems with it was that I didn't do a lot to the bridge, making it look poorly made. Try throwing in some sections of white from some high-tech frigates, or slices of the Paragon's bridge perhaps, and you'll find it looks way more subtle.
And finally, I would really love to weather the pirate cruiser, but I've absolutely no ideas how to do it... Blending options in photoshop?
Beats me, I don't use Photoshop.

Though I've been told frequently to make stuff look better with blending, so go for it. Take a look at some of the stock D-hull sprites compared to their regular sprites for instance, and see how they've been dirtied-up to look weathered and damaged.