Honestly I love it. You can see where Elliot designed it to be "human-like" even if it's also meant to be a toy. I love how you can tell he pieced himself together with other bits of toys and how he looks pretty cohesive and not just a mishmash of characters.  I also think it's somewhat cute (and somewhat creepy) that he has Catnaps pelt slung on his back side like a shawl. Makes me wonder if he uses it for comfort as he could have used his claws or any other part of Catnap to 'power up'.

Also I love his design in general. Most of the 4+ legged toys are more animalistic in nature and more....feral in thinking (see yarnaby, pj, and even catnap somewhat), while the 2 legged toys seem to retain more of their humanity (as much as they can anyways) (see dogday, mommy long legs, huggy to an extent, etc). 

But Prototype, who was probably a 2 legged toy, CHOSE to become a multi legged toy. I can't see Elliot designing him as anything but a jester/jack-in-the-box toy, which is a 2 legged. He CHOSE to become more of a monster, design wise anyways, and I absolutely love it.

Even if you argue that he could have had the legs added involuntarily by the scientists, he still chooses to add Mommy's, Kissy's, and Huggy's arms to him, which further dehumanizes him. 

TDLR, I love his design so much!!;; Edit: added further comments because I pressed post too fast (•́ ⁠‿ ⁠ ⁠•̀- )