If you're looking for consistency and simpler integration between the devices, go for the iPhone. If you're interested in greater flexibility in your smartphone because you need different functionality in the two devices, go for an android smartphone.
Personally, I've seen no reason to switch from an Android phone to the iPhone after getting my iPad. My phone is more "customizable" than the iPhone and the fact that the iPhone has many more apps available than the Android phone is irrelevant. Among the thousands of android apps available, I have all I need. (About 125) And the simple integration with Google is a plus for me.
I don't, for example, need to have a serious note taking app on my phone. I don't sketch on my phone. And while I can play Angry Birds on my android phone, I much prefer games on the iPad.
On the other hand, I have turn-by-turn voice navigation on my phone, far superior to the navigation options on the iPad. My camera on my phone is better than the one on my iPad and better than what I've seen on the iPhone. And when I need to surf the web on my phone, which isn't nearly as common as it used to be before getting the iPad, I have 4G network speed. (I don't tether my iPad to the phone for reasons too complicated to discuss here but if I did, that would be another good reason to have an Android smartphone since that feature is not yet available on the iPhone.)
On the other hand, if I were getting my first smartphone now, I might well opt for the iPhone simply because my familiarity with the iPad would simplify the learning curve.