Would be interesting to know which applications actually have problems with v6 - the example with directly using a v4 IP is more a user error, not an application issue.
I pretty much stopped submitting patches enabling v6 functionality to various projects back in 2005 as everything I cared about was working at that point. (Side note, I was just trying to search a few of those - but seems that period pretty much doesn't exist in search engine caches anymore. I knew the state of preserving internet history is bad, but I didn't expect it to be _that_ bad)