That has been my issue with Dotcloud too, when it works its fine - when it breaks its really difficult to debug. It feels more restricted than the Heroku environment too, so even if I do know what's wrong it can't be fixed.
But, I love competition and these guys are living the dream. Hope they continue to kick ass and add features.
We got a fairly massive growth, and a lot of internal components required to be upscaled much earlier than planned. As we rewrite, optimize, and weed out bugs out of thos components, the timeouts will disappear, and the platform will be faster as a whole.
Just so you know - we are using the "eat your own dog food" principle as much as possible. API, website, docs... are all using the DotCloud platform itself, and we generally don't need escalated privileges to debug stuff. I think we need to be more explanatory about the various ways to inspect logs and debug code, since there is a lot more than meets the eyes :-)
I'm curious about how you feel that we are "more restricted than the Heroku environment"; I would really feel compelled to fix it in any case!
All the best,