I like them both, but for different reasons. The Matrix is a solid action movie and I will always be thankful to it for turning Hollywood away from confusing close up fist fights in action movies, but those Alice in Wonderland references... really? Maybe they did it before it was cliche, but I can't get over it when I rewatch it now.
I think Inception is stronger over all. The action is good, and without ripping off the Matrix, and it's an interesting exercise in analysis. I just LOVE the bit at the end with the top. People end up getting too caught up in plot details about the various levels, wondering whether or not he finally made it out, when it's telling you NOT to obsess in the end.