Unlike some users here, I see the necessity for various security features such as sudp, privilege separation and permissions. Yeah, its a PITA, but I would rather run BSD, Linux and IRIX, which are at least *somewhat* ready for a security-conscious person, than AmigaOS. In addition, on the aforementioned OSes I can easily setup shell and Perl scripts to run automatically using the system function crontab but if I need to run them on demand all I need to do is make sure their location is in my shell's PATH.
Similarly I have access to significantly more advanced filesystem,. I have never seen an Amiga filesystem support soft updates, for example, and those are safer and easier for me to use, as well as faster and less likely to lose data. I don't know how Amiga filesystems store logs, but it looks like SFS is a 32-bit only equivalent of ext3, PFS and AFFS ( FFS is the BSD name for UFS,so AFFS is standard for Amiga ) are equivalent to the original UFS and ext2, that is no logging or soft updates so the filesystem has to undergo periodic checks on boot and while in use for file fragmentation and possible crash operations. I like soft updates because they ensure disks are atomically written, don't require an fsck before mounting and guarantee filesystem integrity.
Also, just me here, but I like IRIX Magic Desktop just as much as the AmigaOS look. In some ways the GUI is even more flexible, such as the native GL-acceleration allows for transparency and desktop effects without relying on DRI, which is basically a nasty hack over X11. The desktop of IRIX is one of the reasons I continue using IRIX, as it has the right amount of usability and customisable look, using the .Xdefaults file.
Using an NG Amiga would require a damn convincing reason to spend 6 times what I would pay for a top of the line SGI, for comparable performance, that's why I await 4.2+ and SMP/64-bit support/memory protection