HipChat's fatal flaw, IMHO, is publicly-accessible file downloads, even in private conversation, with no ostensible lifespan (that I've seen). While the URL for shared files might be extremely hard to guess, I can never feel comfortable not being able to predict what files someone might openly share.
Agreed. Also, coming from iChat before Hipchat, sending files on the same network was so fast. I hate that Hipchat requires me to upload the file to an external server... It's handy for members of our team that are out of office though. I'd rather everyone's files ended up on our internal server, even if it was a little slower for outsiders.