Well I guess I coulda squinted, but I already saw the movie once in IMAX, and squinting doesn't do much good when the movie is 3 stories tall.
In any case, the images move fast enough that, unless you're really looking, the CG is not overly apparent. I think it flows well. Those that go looking for CG and related "quirks" like changing backgrounds, will find them, especially with the DVD set in slo-mo. But considering that Reloaded has some of the most complex visuals ever created (right up there with LOTR), I'd say they did a bang-up job.
One of the things I found out from watching the extras was that there's more CG than you might think. For example, many of the vehicles on the freeway were CG, especially where Trinity is dodging them with the motorcycle. I had no idea.