No need to worry about roms with amithlon. Its different to uae in that you dont need to configure it to your liking. The kickstart rom comes with the package and is dealt with automatically.
Harddrive space: Thats up to to you, but amithlon files total about 3meg. Anything using UAE needs considerably more (although still a negligable amount). OS3.9 I believe is only about 25meg.
Hardware compatibilty: The one area that uae has an advantage. Amithlon is more or less restricted to p2/p3/p4/athlon/athlon xp/athlon64/core/core2duo/core2quad/phenom/phenom2/athlon2 type machines with tnt/tnt2/gf/gf2/gf3/gf4/gf5/matrox g100/g200/g400/g450/g550 for gfx and ac97/sb128/sblive/audigy/audigy2 (plus any hardware that a real 68k machine has drivers for). Other graphics cards are supported, but with limited support. There's also other sound support via linux drivers, but you then lose DMA for that device.
Installation: actually pretty easy to set up amithlon. The entire process, including updating kernel and installing OS3.9 takes about 10 minutes when you know what youre doing (although to be honest it can be a little confusing at 1st).
Compatibility: Amithlon has no custom chipset emulation, so relies on 68k uae for old games, etc.
Speed: No contest. Amithlon is, and probably always will be faster than any other amiga emulation. Not just because of lack of custom chips to emulate, but amithlon gives you direct hardware access, something no version of UAE does. Write to ram in amithlon and ram gets written to directly, no need to emulate memory busses, chipset timing, etc. Same is true with gfx, sound, nic, etc.
Screenomdes: Using Amithlon you can create your own using p96mode. With UAE youre restricted to the modes that come with the p96 driver.
As for amithlon's "special version" of os3.9, its actually pretty similar, just with a few extra files for amithlon devices and so on, not to mention it also comes with BB1.
In a nutsehll if you want a "serious" dedicated amiga os system amithlon is a better option. If youre more interested in old custom chipset games then some form of uae might be a better bet (although 68k uae works nicely using amithlon/os3.9).