you're shooting with the wrong body, and by and large, Canon's AF system on their semi-pro level bodies (40D, etc.) are a lot slower than comparable Nikkor offerings (D200, etc.)
It took 6 pages, but someone's finally got my point. Thank-you.
I assume this is based on personal experience?
I work in a camera store and I've gotten to play with pretty much everything Nikon and Canon have to offer.
Canon's 1D and 1Ds are amazing for auto focus. Fast, accurate and just all around impressive. 5D mark II and below, not nearly as impressive. The 5DII is the same focusing system as the original 5D.
I even find a Nikon D90 more accurate than a 5DII, but the focusing system in the D300 and up is simply amazing. The 51 focusing points is a bit over kill, but it does give a large amount of control over where you want to focus. I don't find the focusing speeds any slower than Canon, not sure if it's any faster, just more accurate with the same speed.
But, I will agree, the lenses make a huge difference. It's not the AF-S alone that increases focusing speed. The Silent Wave Motor is what makes it quieter and faster, and not every AF-S lens has it, and not every SWM is created equal. The SWM in the 18-55 for instance, and I steal this right from Nikon's site, "Incorporates a newly developed compact SWM (Silent Wave Motor) for quiet focusing", it's a more compact version. Not quite as effective.
Anyway, hope that helps.