The hardware has not changed, so..
Perhaps it's time to factory reset. If you're rooted, just back up with Titanium Backup and restore after if you like.
You can also try a custom kernel that has dynamic fsync or disable fsync, that'll help on IO lag. However, it won't fix it entirely. Factory reset should help there.
Tegra 3 has some bad IO problems, and the storage chips in the Nexus 7 16gb sucks, although you say you have the 32G so I'm surprised there's an issue there. But it's manageable. Trust me, mine drives me nuts too sometimes, so I factory reset about every 4-5 months, depends on when it starts pissing me off.