I heard someone explain it like this: Lillie fulfills the role of the childhood friend love interest in your average anime, but they didn't make a difference for her interactions based on gender, so this is the closest to actual yuri you can get in Pokemon.
^Iruru's design actually changes a bit after a while, while her proportions are stil "cool-sensei style" she looks more like a teenager currently, which works, as her role in the family is the teenage daughter.
Tomoko being comfortable enough around Asuka to be her usual gross idiot self is just as much character development as her learning to interact with anyone else like a semi-normal human being.