Oh god. That song and dance sequence hurt my brain.
The weird thing is that Mew would then supposedly be the ancestor to birds, reptiles, mammals, insects, inanimate objects etc.. It would be more likely that Mew is itself the descendant of some sort of common ancestor who lived ages ago, but retained a lot of common traits because of a lack of selective pressures. Kind of like how sharks remained largely unchanged for hundreds of millions of years, despite - in the meantime - dinosaurs rising up, going extinct, being replaced by birds and especially mammals taking over and so on. Mew would be a living fossil, perhaps, but not the common ancestor.
More seriously, thanks for posting that Darwin quote around 9:20 (although according to a cursory Google search it seems it isn't actually one of his but just commonly misattributed to him; it's still a valid point). Many people who misunderstand evolution today do so because of this idea that it necessarily leads to what we as humans would class as "better". With such a misunderstanding, it would not make sense for animals to lose their eyes or grow smaller or weaker as part of their evolutionary development. Because we'd then expect everything to get "better" according to what we would value. Having sight would be "better", right? Being bigger would be "better"? Well, not always. It depends on the circumstances. Not on our own notions of what "better" should mean.