I've always thought that Mewtwo just looked weird. I thought that the tube behind his head looked awkward, I didn't understand why he seemed to have massive chest bones, he seemed disproportionate to me, and I never understood why his fingertips were balls. Overall, he looked rather unimpressive. I later learned that his appearance was heavily based off of Giygas (Mother 1/Earthbound 0) who's appearance appears to have been inspired by Frieza from Dragonball Z. This makes Mewtwo seem rather uninspired to me.
Arceus, on the other hand, looks better in my opinion. He has a strange golden "ring" around him adorned with green spots that look like jewels, a cloud-like fur, golden feet, and he can change his type and appearance with the plates to boot. Furthermore, he is based off of a Chinese mythical creature called a Qilin, and Arceus' myth is similar to that of Pangu, the Chinese creation deity. That sounds more interesting than being a lab experiment.