Both kernels are very stable, so you should experience little problem there. Also, Linux has released 2.0.0 source, so, regardless of which baseline you obtain, there's room for some upgrading.
The major areas of difference between the two packages are the ease of installation and the ability to track current Linux/AXP development efforts. Linux on the Alpha currently supports the statically-linked ECOFF object file format. Work is progressing on ELF support (while not eschewing ECOFF, which provides compatibility with DEC Unix (a.k.a., OSF/1)), as well as use of the glibc libraries. Red Hat, possibly because they run the mail group, seem very involved. Craftworks seems aware of developments and is working on FORTRAN.
As I was upgrading Red Hat, I had the chance to use glint/rpm. You get much tighter control over what is being installed, to the point of saying ``yes, I want Emacs'', rather than the uninformative ``Base Installation''. Craftworks, too, has an upgrade installation package (CRAFT), but Beta 1 was not compatible with it, so I did a full install.
Craftworks' strength, however, is in the creation of associative file systems. A panel appears with /, /usr, /home, /local, /pub and swap defined as potential mount points. For each, you can specify that it is hosted on a different partition/hard drive. This allows for great flexibility in splitting operating systems between hard drives. The information is naturally saved to the /etc/fstab file.
Red Hat finally includes the TGA device driver for X-windows. Sadly, knowledge was not passed down to the install program, so you have to manually install it afterwards.
LaserMoon has decided to delay the release of its Alpha port until shared libraries are available, pointing out that the lack of this capability is a real performance hit for what should be a very high performance platform.