I bought into the "Nikon has better glass" thing which is how I got here. But I think knowing what I would know now, I would say "Nikon has better mid tier glass". The 400 4.5, 600PF, and 800PF are budget marvels. If you're in the $5K - $10K range, I don't think a better system exists for wildlife photography.
However, if you have a 400TC or 600TC - you'll always get better quality images from those lenses, which means there often isn't a reason to have the 400 4.5, 600PF or 800PF unless you just want to save weight.
At the top end (think $15K+ budget) most people are going to have their 400 f2.8 or 600 f4 that all brands have, and while the built in TC is really nice - I value precapture raw, more FPS, better AF, etc. more than that built in TC. in most cases you're paying $3K USD+ for that built in TC as well, which can get you a lot of other glass, bodies, or accessories (CF cards).
My expectation (and I'll post more when I learn if I was right or wrong) is that the A1 II + 300GM + 600GM combo will outperform any of Nikon's current offerings for the majority of people.
Even adapting my 300GM to Nikon bodies (which means reduced image stabilization and AF), the 300GM with TC outperforms both the 400 4.5 and 600PF, meaning those don't provide much, if any value.