Adding your own content to games made with The 3D Gamemaker™ is difficult, to say the least, but I tried to customise as much as I could.

It encourages you to choose from a bunch of pre-made player characters, enemies, bullets, items, bosses and environments. There's a user bank as well, which requires you to make your own .x files in another program. As far as I can tell, there's no way to directly set the genre or the controls, the program assumes what it will be based on the player object. You are right that the eyeball was hacked together: adding legs to things is a 'feature' of the program that I was forced to utilise as it was the only way to stop the sphere meeting the ground at its point of origin (i.e. the eyeball would constantly be halfway through the floor). It's also possible to add wings or wheels to any player object, but I think doing so might radically alter gameplay.

As EffBee said, if you don't want to use one of the pre-made levels, the level editor is capable only of creating maze-like corridors that don't even allow for properly tiling textures (as seen in my game). If you go deep enough into the program's menus, there's a way to manually set the locations of enemies and items, which I did. Otherwise, the game just places them randomly and you end up with health packs everywhere.

Art-wise, I did the textures for the environment and the eyeball (which you never actually get to see due to the 'wacky' camera) but every other 3D model appears as it came with the program. You can mess with enemy behaviours and variables to some degree, which I did, but you can't change an awful lot in that department.

I found no way to alter the lives/energy/score thing. You can change the colour of the text. If you make a racing game, it adds a variable for laps. That's about it. You can choose from three win conditions (touch end tile, kill all enemies, collect all items), none of which I particularly like. I also couldn't find any way to change the lame 'congratulations' text that you get upon meeting the win condition.

The in-game music is Soda Pop by Britney Spears slowed down using paulstretch. This is in the spirit of the original Eyeball game, which used a poorly sequenced MIDI of that song. I think that's everything?

Congratulations! I was just uploading a video on the assumption that you'd never get it to work. It will still be a good thing to have if others have trouble, though. Very nice to have this fix, though, as the game had even stopped working for me (it only ran properly the first time I opened it).

The spiders were supposed to spit webs! Must be a bug I overlooked. But yeah, the skeletons and the Cyclops are both supposed to throw knives... with terrible aim, I might add. The bosses are among the least configurable things in the software, so that Cyclops is basically as good as I could make it, as far as I could figure out at least. He's underwhelming, I agree... though his choice of attire certainly isn't.

Looks like zero-distance fog?

The game displayed fine for me although the player bullet texture was slightly brighter than normal it would seem, making the square borders of the texture somewhat visible.