I've never used a Nikon so I will not engage in discussing them.
Since you asked specifically about Canon (and since this is a Canon forum) I will try to actually give you some feedback!
Of the two bodies you mentioned I'd recommend the 1D3 -- people talk about AF problems when it first came out and they addressed those problems with both a hardware fix and a software fix. To this day it is very highly regarded both in performance and image quality. And, some of the upgraded features on the 1D3 make it a nice choice over the 1D2(N).
If your Pentax struggles with action shots (is it a 4:3 mirrorless camera?) then yeah a DSLR will win the day.
Alternatives to the 1D3 in the Canon lineup are the less expensive 7D with a newly designed autofocus system that puts it up there close to the 1D bodies, and then the 60D, again lower-priced and with the older AF system but no slouch in performance. Any of these cameras, paired with a good lens or two, will show a real edge in capturing sports/action, so I'd say it's what you can afford, as long as you budget in a good lens, such as the 85mm f/1.8 and/or a 70-200 -- both very highly regarded for sports and action shooting (other lenses may perform fine but you can also end up with lenses that suck for these things -- look for lenses with very good reputations).