I'm not really bothered with the lack of flash support to be honest, mainly because I barely visit any sites that utilize flash. And when I do, there's always my laptop for that.
My biggest gripe though, is that on some forums I frequent, my posts end up looking like a gigantic wall of text because for some reason, I can't paragraph on my iPad, so I end up having to edit my posts on my laptop. Which is annoying because it's inconvenient doing things that require 2 devices instead of just 1. But thankfully though, I don't have this problem with all the forums I frequent, like this one and Gaia Online.
Another gripe is the lack of multi-tasking. It's annoying every time I need to use 2 apps at the same time, and I have to get out of the app I'm using and go to the other one, then return back to the previous app.