No major pitfalls that I haven't been able to overcome easily. Use hosted mode heavily.
As you are using GWT-ext you will almost never need to touch CSS yourself unless you want to tweak the out of the box look.
My recommendation is to use a GWT "native" widget over a library one where they are close in features.
Re search engine indexing: yes the site will not have navigable URLs normally (unless you are only adding widgets to elements of a regular web site). You can do history back/forward functionality though.
