I think that the "problem" with the stock wheels is that they're heavy. I still ride the front wheel that came with the bike and it is noticeably heavier than my other wheels. I don't have the rear wheel anymore because it got trashed when I got hit by a car. I still have the hub though and it's like an anchor.
For me the wheels that come with the bike are fine to ride but they're not the lightest set around by a longshot. I don't find them to be flimsy at all.