Is it unusual for a prospective university to offer a bonus to your stipend after visiting?
It's not too unusual. Lower-ranked schools know they need to work a little harder to attract top talent. For example, I did an REU at a lower-ranked school, and they admitted that the only reason they bothered offering an REU program was hoping that some of us would become grad students -- they normally couldn't attract grad students of our caliber. Offering a 15% stipend increase to particularly promising students seems altogether appropriate.
University 2. I might seriously consider university 1 if you didn't like university 2 for some reason -- what you do is far more important than where you go, and getting into a top school does not guarantee you an academic future (not even close!!). But in your case, both seem like good options, so if you get into university 2, I would go there.