"Graceful degradation" is pretty important, and there is no way to even display Flash if a user doesn't have a player. Whereas, it is at least possible to do fancy things with AJAX that can be dumbed-down for clients that do not support JavaScript.
I've never used Flash extensively so I'm not sure of the exact pros and cons of each, but as a user, I will go out of my way to avoid sites that use Flash. Javascript can display photos just fine, and doesn't slow down my entire computer.
Any sort of fancy transitions flash gives you more options(easily).