The main things I miss are better google voice integration on the nexus phones (the ability to use the web interface for texting is something I can't give up). I also used to not pay for texting this way and could actually afford to have a smart phone because of it since Tmobile has a $30 no contract 100min/unlimited data plan for unsubsidized phones.
I also needed some sort of google talk app which I finally found with the $5 version of the verbs app. A bunch of people I communicate with are on android and use google chat instead of facebook chat or imessage.
The current iPhone does some things much better. The biggest thing is battery life which is at least twice as good as any nexus phone I've used (probably even more). The difference in battery is really incredible. The new native Facebook iOS app is also great to use. The iPhone hardware is also subjectively much nicer, it both looks and feels a lot better to me - makes me wish Google had partnered with Nokia.
Really though they're both pretty equivalent at the point.
Edit: Almost forgot, the critical feature of android was turn by turn navigation which apple finally came out with in iOS6. Now that google's released their maps app as well the core differences that mattered are gone.