The thing is, unlike other games where you're hopping between gear and such, a ship is a long term investment. I'm still using my Intrepid I got years ago, as well as my raptor I got for my Klingon character. So $25 in my mind is reasonable. And I'm the first to yell murder when I see Cash shop prices in games. Rarely will you be switching ships on the fly since you build your character, Boffs, etc. around that ship. Think of your ship as your "Character". Of course if you're the type that likes switching ships a lot then yes $25 is a bit much. Also, the level 41 (or what ever it is, is still viable.
The only slightly better ship is a Fleet Ship (however that can be argued).
The only cash shop ships I'd say are not worth it are the lower tier ones like the alternate Nova and such.