Wipeout2097 amiga vesion is ppc only. You can howver play the playstation version on os3.x with FPSE.
Joypad should work if you have usb hardware supported by poseidon. Additionally you can use a catweasel and use 9pin amiga joysticks/joypads.
As for what OS4.x and MOS do that amithlon/winuae+os3.9 cant, to be honest, not a lot. The main difference is mos/os4.x do more "out-of-the-box" whereas os3.9 needs the user to make lots of modifications. Given similar hardware resources all 3 are similarly capable. The main exception that stands out is web browsing is a a better experience on OS4,aros, and espeically mos.
As for how fast it'll be on an athlonxp 3000+, pretty darn fast. For 68k speed it should give something along the lines of a 1ghz g4 using ppc code. You should be able to run dvd-ish quality movies, but no higher. Faster again when using amithlon native x86 code, but that's more theoretical as so far there's very few amithlon native apps.
As for warp3d/open gl, unfortunately there's only software rendering availbable for amithlon via wazp3d (technically not true, but for conversations sake t may as well be). Its quite fast for a cpu renderer, but obviously nowhere near as fast as 3d gfx card rendered. In quake 1 on my amithlon box I get about 190fps in 640x480 with normal cpu renderer and it drops back to about 50 using wazp3d with all effects enabled @ 640x480 (filtering, fog, mipmapping, antialiasing, etc.). Payback runs fine at 1600x1200 in normal software rendering normally, but I have to drop it back to 720x576 using wazp3d (still looks nicer using wazp3d though with effects enabled).
As for usb/ps2, personally I use usb mouse and keyboard, but I had to enable legacy support in bios as otherwise it'll rely on amiga os usb stack. It's also completely p96 and ahi based. 98% of system friendly apps work fine out of the box.
I think people underestimate just how much software is, or can be system friendly on the amiga too. Stuff like Genetic Species, Flyin' High, Racer, SimCity 2000, can be played without UAE, not to mention the more typically mention things like Trapped, Trapped2, Gloom series, ScummVM, NemacIV, Napalm, Earth2140, Racer, doom, heretic, hexen, seuck (this was a surpise to me atually), Dynamite, mame, snes9x, dgen, quake, quake2, payback, descent1/2, descent freespace, Foundation, Exodus, Shadow Of A Third Moon, Onescapee, Virtual GP, Tales From Heaven, Nightlong and so on and so forth. There's a heck of a lot of system friendly stuff out there that doesnt require UAE. More apps then games, but still a lot of games too.