GREAT to see stuff from you again, Ben

I love the way you are doing this anime-ish style, it is a LOT cleaner than your earlier stuff, and it shows you have learnt a lot about color theory, I hope you keep showing us stuff like this

. Personally, I dont see what looks bat at all about the anime eyes, you are obviously going for an anime style and the eyes work great within that, also helps separate the "holy" humans from the rest.(Love the creepy smile on Skull guy)
I think the whole problem with the feet is mostly how everything is outlined, but the feet's sole isnt. You could try playing with the shading to see if that defines em a little better.
I have to say I dont see why you didnt like the first Chimbie version(tho I havent played trough CaveStory), I find him very creepy in a cute sort of way. I went and parodied him emphasizing what I like about it to see if maybe that gives you some ideas. I wanted to make him a little disgusting and selfish looking :p

I also went and played with the shading on the Morrolite's robe a little....
PS:GOD photobucket is AAASLOOOOW today ¬_¬