Emulating the timing of the registers is a mess... I wanted to fix that problem too, but since I didn't write the original code, it made absolutely no sense to me. I'm hoping David will have a chance to rewrite that code. Red Alarm is kinda playable as it is... 3D Tetris is worse, but almost playable... Golf is unplayable because it doesn't freeze the screen like it should. That's the same problem that causes 3D Battlesnake not to work (and probably Etch A Sketch, and other homebrew direct screen drawing apps that disable the framebuffer refresh).
The frontend uses an old manifest file from VC6 to enable the XP look and feel. I suspect that is what is causing issues with XP64. I will fix the missing parameter and stop RB from exiting when passed a bad parameter. I agree it is a little harsh right now.
What speed is your PC? Running some games in 3D mode takes a lot of juice... nothing really wrong with the emu except that it's not optimized very well.
About joystick support, a utility like joytokey works well.
Hmm... upgrade, or start optimizing Reality Boy ;) . 2D runs fine on my Core2Duo 2GHz w/ 2GB RAM laptop, but 3D Wario Land is still somewhat slow motion. I assume a faster CPU would speed things up, although there's no multithreaded processing, so it wouldn't run any faster with more cores, other than the ability to dedicate an entire core's processing to Reality Boy.
If you just want it to play at full speed and don't mind some of the annoying effects, you could use the frameskip option (-frmskp (0-9) )... on my laptop a -frmskp 1 runs full speed, but you get the problem of flashing graphics (single frame) disappearing or not flashing, depending which frame is skipped (if you get injured, sometimes you'll be invisible, other times you'll be solid like nothing happened). At -frmskp 2, you don't have the single frame flashing problem, but screens that have animations of 3 frames look to stand still... like the propeller on the main Wario Land screen. It also starts to look kinda choppy after a couple frame skips.
You can see how many FPS it's running at by pressing 0. I don't know if there's a problem with the frame counter or the throttle, but on my laptop it seems to report 46FPS when it's running full speed, even though it should be running at 50FPS.