The creation of the Mew Mews is more scientifically plausible than one would think, though it's not quite LEGO Genetics in real life, you wouldn't turn anyone into a magical girl, and Ryou would probably die by the age of twenty due to his incompatible genes.
With the introduction of the Mew Berry Rod, we can assume that Ryou has constructed all the previous weapons as well, ruling out the theory of magic being the cause behind the materialization of their weapons. Nanotechnology would better explain this.
In addition, this would also explain why Ichigo and the other girls have to call out punny names when summoning their weapons. Voice-activated nanobots.
Porpoises are victimized by dolphins just for being different; see Retasu.
Some Bible scholars posit that the Fruit of the Knowledge of Good and Evil was a pomegranate; see Zakuro.
The Mew Mews' outfits designs being a tad risqué and flashy make sense since while Ryo's a genius, he's still a teenager boy. It's a wonder how Ichigo hasn't chewed him out for it.
The first monster in the seires is a mutated rat. And, in real life, cats eat rats, explaining how Ichigo was able to take him down with ease.
The reveal that Deep Blue is actually Aoyama actually explains why all the alien activity centers around Tokyo. The aliens get their orders from a being that lives in the mind of a 13 year old in Tokyo; it wouldn't be a stretch to assume that Deep Blue doesn't know much about the rest of the planet at all.
He's still alive in Re-Turn, albeit without the marking that he usually hid with a collar, so it looks like he and Keiichirou figured out how to reverse it.
In episode 17, Quiche turns up at Ichigo's window and tries to take her with him. He knows where she lives, which probably means he's been stalking her all the way to her house. He also knows where Cafe Mew Mew is (the only alien to know until he told Pie and Tart). How much time has he spent stalking Ichigo?
The backstory of the aliens in general is extremely sad, but it gets worse when you consider the fact that, despite being desperate, only three of them could go on the mission. One being a child. Just how low are their numbers?