I think that may be part of the intention? Definitely in Adventure Time's case. It seems to be deliberately using the cartoony style as a way of highlighting the horror of the world in which Finn lives.
The fact that those shows are written and structured well doesn't make the art style a good choice. In SU's case it holds the series back, nothing about SU is the dopey comedy show the art implies it is.
It feels a lot more dissonant to me in SU, since Adventure Time's world just has more of the chaos and sociopathy you expect from a cartoon world that's not quite so tightly structured. Of course, I haven't seen a lot of AT and I've seen all of SU so far, so.
I have no doubt that the look helped SU actually happen, since it makes the series look more like an Adventure Time than, well, a ThunderCats 2011, both in the programming block and in the budget. I also think some of the ugliness plays into the thematic ideas that reality is messy and no one is perfect, etc. in ways that, like, an idealized superhero look or something couldn't, comically undercutting these otherwise complex and human characters and working against the general cultural notion that heroes have to be pretty. And it's animated well and there's some occasionally good action in there.
But there's also a whole segment of viewers of the genre that it is that it's not going to reach that way, despite its phenomenal content under the surface, and that's kinda unfortunate. Plus I have to look at it to get the story. = P