wow, that's a tough one! I'll try to do my best:
1. stability: both systems have a reputation of being very stable. however, the stability of the os isn't everything. you need stable hardware, drivers and application software as well.
2. ease of use: depends on your present knowledge. a modern linux distribution featuring KDE 2.0 looks very much like WinXX, but don't get carried away: there is much more to linux than KDE!
OS2 on the other hand with it's object oriented work place shell is more on the Mac side (if anything). os2 comes with a nice tutorial that takes you through the basics.
3. system requirements: Warp 3 is a pretty old os dating from 1994 and only has "minimal" requirements by today's standards. any computer capable of running Win95 will do nicely.
4. tools: I guess, linux wins this one hands down :-) every linux distribution has several CD-ROMs full of tools and utilities. however, the sheer number of tools available doesn't mean, they are all useful for your needs.
all of the tools you mention are in linux as well as Warp 3 (Connect)
5. mousekeys: os2 has several enhancements for the handicapped like "sticky" keys. I don't know about mousekeys.
6. networking: this one as well goes to linux, it being much more recent than the oldtimer Warp 3.
The comparison would be much fairer between a more up-to-date Warp version like Serenity Systems eComStation aka Warp 4.5.