On a more serious note, I think the reason they went with a new design for the Great Fox II rather than going with something resembling the old design... funds.
The Great Fox was NOT a cheap machine. James McCloud left Fox an 80-year Mortgage behind on the damn thing when he died. It may be gone, but Fox will still be paying for it for the rest of his life. He had to go with something smaller, and cheaper.
As for Star Wolf, I'm really not surprised that they lived. All we saw was them leading away a bunch of enemies so that you could go for the queen. They're a competent crew, and while the things looked intimidating, they could be killed. It was just that Fox and them didn't really have time to deal with it, they needed to get to the Queen, so Wolf took Panther and Leon and opened the path for 'em.
As for Peppy, gogo escape pod. If you'll notice, the front of the escape pod Peppy shows up in looks suspiciously like the external view of the Great Fox's bridge. Peppy never had to move anywhere, he just fired the thing up and got the heck outta dodge before the rest of the Great Fox ker-sploded.
I like the touch with his bandaged cheek and arm where the parts of him that were starting to look Aparoid-y obviously 'sploded with the Queen.