Most of the personified programs have titles that reflect function, like the Oracle, the Keymaker, and the Architect. But then we find an "old" program called "The Merovingian." Say what? Are you telling me Charlemagne had a computer? The character/program's function would have been perfectly expressed by a title like "The Keeper," "The Collector," or even "The Miser," but someone threw in "Merovingian" just because it sounded cool and not because it fit in with the total design.
Inconsistent handling of the Matrix bugs me also. I understand that story needs require that the rebels need their virtual phone connections to get out of the Matrix instead of just jacking out when danger threatens, but then you can drive out via the "freeway"? (Flashback here to "True Stories of the Information Highway Patrol"--those of you who were at WisCon will understand--.) The freeway is just an excuse to have an overdone (and overlong) car-chase in an otherwise cyberpunk environment.
Apparently, being a slave to the Matrix is good for you, as evinced by the scenes in Zion, where everyone is buff and young-looking, with the sole exception being SF-movie veteran Anthony Zerbe as the aging Councilor Hamman. (And why should the machines cause the slaves of the Matrix to develop muscle tone at all, in their artificial wombs?)
Being in the Matrix is handled inconsistently. If you die in the Matrix, your body dies, but dropping out of contact when passing through one of the Keymaker's "back doors" causes no problems.
Does it make sense to diable the alarms on a virtual building by cutting off the virtual electricity (by blowing up a virtual power plant with a virtual bomb--)? Even if you consider this as metaphorical cyberspace representations of actions that are actually attacks on lines of code, it doesn't seem to be sensible.
That said, the film is still fun to watch. Neo's battle with the seemingly infinitely replicating former agent Smith was particularly good. The major plot twist at the climax was a surprise, and, although we are given some hints, this second installment of course ends with a cliffhanger. I look forward to seeing the third episode in December, but I'll be taking along some serious earplugs.