"but there's no rational basis whatsoever for him being fucking telekinetic in the real world." - wrong
Didn't you notice the huge metal plate / computer interface grown into the back of his skull since childbirth?
I believe that Layth is entirely correct; and it amazes me that everyone, especially geeks, freak out about this so much.
Why people today are somehow shocked by human (using high tech electronics) being able to wirelessly communicate with computers to send a message (in this case: SELF-DESTRUCT) is beyond me. Radio chips are the size of a penny NOW.
Neo never does telekinetics in the real world, he uses a wireless backdoor to send commands to nearby computers, not shocking; he also does some simple low-res augmented reality overlay to give him a visual representation in 3D space of other wirelessly connected pieces of electronics, also not shocking.
Why is it deemed unlikely that the Oracle reprogrammed Neo to perform a task (either one more loop through the cycle, or a more definitive change to the world). We're shown computer programs in the Matrix using food as a code delivery mechanism into human brains with the cake->orgasm scene. Still not shocking.
And as for the whole agent Smith taking over a human thing: with that much electronic hardware in their brains, what's to say that the plug-in couldn't take over the motor/sensory control portions of the brain. The host's higher-functioning portions of his brain are still his own, it just isn't in control; the software running on the receiving side of the plug is (a pity Dollhouse couldn't stick to that kind of model...). I'm still not shocked.
When it comes down to it, the end of the first Matrix movie was shallow and pointless (Neo takes over the holodeck!!). The sequels had some horrible flaws (questionable CGI, painfully long fight/chase scenes, heavy handed music, etc...), but it gives a far better ending than the first movie.
