I don't know if it's been fixed since I noticed it, but at least some version of it is lacking the ability to enable/disable UPnP support at compile-time.
This has been fixed, you can provide USE_UPNP=XXX to the qmake script (see the qt readme).
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It also adds an implementation of bitcoin: URIs that is not compatible with the existing established/in-use standard.
It's just a wiki page, not a standard. In my (and Gavin's and many others) opionion URLs should be as simple as possible. The 1243X45 exponent stuff is simply arcane.
I do agree more standardization should happen, an "official" Bitcoin URL format would be an interesting subject for a BEP. When that standard format is determined, it will of course be integrated into the client.
Until then, we chose the most simple format possible, which can be described in one line: bitcoin:?label=