Don't watch the Matrix trilogy. Watch the Matrix. Pretend the other 2 never existed. Well, watch the second if you're really desperate.
Agreed. They went really overboard with the obvious Jesus metaphor in the second + third films. Revolutions remains the single worst 'franchise' picture I've ever seen, including the prequels.
Toy Story 3 > Inception. For me at least.
The Matrix is undoubtedly the best of the three, but that's mainly due to the inherent problems of the narrative. The journey is always more interesting than the result.
This is most easily seen if you ever play RPGs. The best part of the game is always when you're slowly learning and building your way up. Once you finally reach that illuminated over-powered state, it's fun for about 15 minutes but then you just get bored. The Matrix has the same problems; the most interesting part of the first is the struggle and the awakening of Neo. Once he becomes the One, there's very few ways you can keep it interesting.
I think there's some good ideas in the last two films, but they're hampered by this and ultimately the crew just resort to making films with the style of the first but without much of the substance.
I might work up the energy to watch Inception today. I suppose I should see what all the fuss is about.