I think you have to expect APC to sound like Tool, I mean come on they have the same lead singer.
Tool although, is much more dynamic in their songs. Danny Carey is amazing, and does things to the songs that APC can never make me feel.
I love both bands, but like someone else said, APC is more "short and sweet."
btw, I have front row seats to the APC show Nov. 18th, it's at my University
edit: Have you guys heard the Tilling my Grave remix of Weak and Powerless? It's off the underworld soundtrack I believe. Also, for those who haven't heard this CD yet (13th Step), check out The Outsider, Blue, and The Pet. Those are my favorites