Gabe, you not making it easy for me
Hah, it's really not an easy decision.
Like many, I would suggest you try both before committing to a system. While the Phase might offer incrementally better IQ (a fairly negligible 4Mp advantage), the ergonomics and general functionality of the Aptus-II exceeds the P+ in spades. If you're shooting with a 645DF, this is essentially meaningless, but if you're shooting with a technical camera, this can be a fairly big deal, as it's not always easy to tell if you've nailed your correct focus point, or if you've tilted too much.
That said, the Aptus-II is finicky by comparison to the P+. It doesn't like many CF cards other than San Disk Extreme Pro cards. While it is fully supported by C1, I find updating the firmware, still to be a PITA, as the camera will oddly disconnect over and over before actually working. P+? Never had this issue. P+ has a robust ability to format CF cards in the camera, and shoot essentially whatever kind of CF card you're using. The Aptus-II CF cards need to be prepared on a computer. Most all of the documentation and support for the Aptus-II is extensively Mac-friendly. Coming from a PC-user, this annoys the hell out of me. That said, the files themselves work seamlessly with C1, and updating the firmware really isn't a common endeavor. And if you shoot exclusively with San Disk Extreme Pro cads, you'll never have an issue with Leaf.
I also have issues getting the colors "right" with the Leaf back. While there are literally dozens of profiles/options available, without a Mac and Leaf Capture, it is not possible to customize the color profiles of the camera. Usually auto white balance is fine. However, if you use daylight/tungsten/etc., they will absolutely be uselessly wrong (would be nice to be able to fix this issue without a Mac.).
With all of my gripes out of the way, I still prefer the Aptus-II, due to its increased functionality. I am, however, greatly tempted to ditch it for a Credo, as I speculate most all of my concerns will be absolved at that point.