The "villain" of Lilo and Stitch is, rather directly, societies and social systems that write people off and do not provide support and care.
It is obvious to the audience -- and deliberately presented this way by the film -- that it is better for Lilo to stay with her sister, even if her sister is a bit of a mess and not financially stable. Mr. Bubbles is not evil. He is there because he wants what's best for Lilo, and he is not unreasonable to think that the sister without a job who leaves the stove on and whose house nearly burned down two days later is not it. The solution is not to "defeat" Mr. Bubbles; the solution would be for society to help Nani succeed, rather than watch as she fails.
Similarly, no one provided any help to Stitch when he was created and discovered. They wrote him off as an abomination, something too dangerous to be destroyed. They weren't evil, and it wasn't unreasonable to think that the experiment created to be an agent of destruction would be better off scrapped. But what would have happened if they had at least tried?
Lilo and Stitch are two characters who were caught in systems that were cold, uncaring, and unsupportive, even if the people in them were not evil and were, in fact, just doing their best.
It's a movie about people who have been written off finding one another and building a found family where they can get and give the support and care they didn't get from the people with authority and I love it so much.
