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.
As mentioned before, Ryou's incompatible genes will kill him by the age of 20. Ryou is already 15
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?