Agency vs. Startup: From a Young Designer
blog.prototypr.io
blog.prototypr.io
The main things in favour of working at a company (start-up or otherwise) are more creative control and the opportunity to perfect something as there's one focus for a sustained period of time.
A lot of professions have this wide vs deep argument for people at the start of their career. I don't particularly buy that either one is particularly "better" over the long-run - capability floats to the top eventually.
I do think culture is key, and particularly how we react and fit into different cultures. I'd have said the size of the agency or start-up is more important - people who come from large companies sometimes find it hard to fit into a small organisations and vice-versa.