My basis for liking Crooked Crosses better than Swastikas for Noddy is that I have listened to both, and decided that Crooked Crosses is superior.
It's far more than just a "remix" album. It's Tibet and Stapleton's attempt at "rescuing" the material on Swastikas, which was a little spare and poorly produced. The songs have been reordered and better arrangements and Stapletonian noise textures have been added which really enhance the album and turn it into something of a psychedelic concept album.
Every track segues into the next with perfect sonic transitions, from the Boyd Rice speech about Nietzschian power struggles to the "Toytown" Noddy children's show theme, to the demented folk collective singalong of "Beausoleil." It just works better, on the whole, than Swastikas.
If you're a completist, you will of course want to have them both. But if you're not, go with Crooked Crosses and consider Swastikas obsolete.