1)Well, your low-cost Nikon lenses are extremely marginal in terms of autofocusing performance. F/5.6 is the MINIMUM aperture for correct AF operation,and your slow kit lens and your slow telephoto lens max out at f/5.6 once past the middle of their range.
I have a lot of experience with the Nikon system,and a few years experiecne with the Canon system. The problem is the D40 has an entry-level AF system with three-area autofocusing, with ONE cross-type sensor--the middle one. It is the cheapest, lowest-specified AF system Nikon currently makes. My wife has a D40,an unless you are using a speedlight with AF assist enabled in dimmer,indoor light or outdoors at something like a patio party, the D40 will hunt and miss,and will autofocus very slowly using a cheap lens like the kit lens, or the 18-105mm, or any other dog-slow,consumer lens. HOWEVER, the D40 focuses very rapidly with the 70-200VR on it, and with the 200mm f/2 VR, the D40 focuses VERY fast, and surely.
The Canon 5D and 20D focus only reasonably well. Indoors, the 5D's highly centrally weighted AF diamond is very poor using the 24-105 f/4 L I have,and it's not all "that" hot with the 50/1.4 or 85/1.8,with slow, indecisive focusing on any point except the central AF point. The same goes for the 20D with the 18-55 kit lens or the 24-105 f/4 L on it. Using a faster lens, like my 50/1.4 or 85/1.8 or 135/2 or 70-200 2.8 L-IS on the 5D, the indoor, low-light AF performance of the 5D and 20D is better than with an f/4 lens; your slow glass is a full stop WORSE, at f/5.6, and the D40 has a primitive AF system. The 5D and 20D and D40 have merely "adequate" AF systems. Compared to the Nikon D1 and D1h and D2x, the Canon 5D and 20D AF systems are slow and very centrally-weighted and virtually useless for off-center AF, or for fast-moving action like track and field.
Nikon's D2x on the other hand was a flagship body, with a VERY fast and capable AF system. Indoors, the D2x will lock focus on ANY AF point selected with about 95% one-press accuracy and speed, even with an old AF dog like a 35-70 f/3.3~4.5 AF Nikkor....but notice the aperture????? f/4.5 minimum.
If you want to see fast AF, you absolutely MUST have a lens that admits more light than f/5.6. With Canons newer 30-40-50D models, the 5D and 20D"s "original" 9-point diamond AF array was updated with the added benefit of the "hidden helper" AF points premiered in the 30D. If you want fast autofocus, the moral is simple: buy a professional level Nikon body, which means $1500-$2500-$4800 entry price, and get away from $100 to $199 consumer lenses. Your entire disappointment with a D40 and cheap lenses is perfectly understandable; the D40 has a weak AF module, but the cheap lenses you've been handicapping it with are compounding the problem. With the 70-200 VR or 300/2.8 or 200/2 VR, even the old D70, as well as the D40, focus lightning fast,and with amazing sureness. Telephoto lenses focus better due to the more in-focus/more out-of-focus nature that aids a phase detection system in gauging "in" and "out",and allows the camera to drive the lens to the most accurately-calculated correct AF point which is how Nikon's AF-S focusing actually works. My wife has the 18-55, 18-105,and 55-200VR lenses and I have used all of those,as well as my pro-grade lenses on the D40. They are slow on the D40; on the D2x, they are MUCH,much faster and more sure and dependable focusers.
The D40 is an entry level camera, but it can focus FAST with pro glass. Combining an entry level camera with entry level glass gives the maximum slowest and worse AF possible. Saying that the D60,D80,D90,and D300 do not focus as fast as "any Canon" is absolutely ridiculous, unless of course you've used (have you,really??) all those Nikons ONLY with cheap, f/5.6 consumer lenses. Nikon's D1 and D2 generation cameras focus better,and faster, and with better user control than any Canon I have ever used,and I have pretty comparable lenses. Nikon's screwdriver 50/1.8 focuses faster than Canon's 50/1.4 USM; Nikon's 85/1.4 focuses faster than Canon's 85/1.8 USM. Nikon's 105/2 DC focuses faster than Canon's 135 2.8 Soft Focus. Canon's 135/2 L is about the same as Nikon's 135/2 DC both optically and speed-wise. I've been at the photography game since the Nikon F2 was the top professional camera,and I have to say that the four years I have been using Canon equipment in addition to Nikon gear I have found that Canon's "consumer grade" cameras like 20D and 5D and 300D have inferior AF systems to those that Nikon has developed since they went to the 11-area AF systems beginning with the D2 series. You need to move away from minimum-specification f/5.6 lenses; they are like racing in second gear; they are holding your camera back very badly,and they will hold back a D40,D60,D80,D90,and D300.
2) Crappy Warranty Service.--Not my experience with Nikon gear. I have had only three pieces of Nikon gear break down in 27 years and over 75 pieces of their lenses and bodies. 1986 a 1969-made 35/1.4's diaphragm quit working. 2004 my D1h's diaphagm stop-down button quit working but the camera still shot and focused 2005-my first-run 70-200VR needed the new,updated electrical grounding system install, free.
3)Quality control issues. Canon had to *invent* autofocus microadjust because their lens QC is so slipshod and the internet buzz about badly focusing Canon lenses was killing them. Canon has so many front/backfocus issues it's almost comical. Not to mention constant Err99 body quirks. And then there's the professional 1D Mark III AF fiasco-that thing still can't focus worth a damn on moving sports subjects; see Robgalbraith.com and download some zip files or atrociously poor AF using a known-good 300/2.8.
There....I addressed all three issues. My advice: stay away from the absolute-CHEAPEST body and the absolute-CHEAPEST, plastic mount lenses if you want performance. Move up to the mid-level bodies and lenses,at least, not the $700, two-lens beginner's kit.