The main one is budget. They're usually pretty slim.
Worst, though (and this is exacerbated by the budget), is a propensity for work to get cut.
Because good animation takes some time, it's often begun before the film hits the edit room. We tend to get involved early. This gives the animator greater sway on the final product but opens up the real likelihood that work will get cast aside.
It's a trade off -creative input vs. financial sensibility. These projects are usually flat fees, there are benefits to the animator to have as much animation as possible in the end piece but at what point do those benefits outweigh the hard costs involved?
In our case, we've tended to take the over-do it route on the animation. On a per project basis this isn't good for cost clearances, but we believe we can link new business and return customers our willingness to explore.
Here is an example of a discarded graphic from WNET/Thirteen's "Curious".