I personally have a philosophy with race bikes - KISS
Really 2 pipes is just to much hassel. Smaller airbox, effects the shock with heat more, and more $ if there is damage.
A friend rides an 05 crf and really does not do a lot of maintenance to it and it has held up really well. I just did a top end, did the valves 2 months ago. only reason they were just barely tight is the aftermarket cam. it has been a really good bike.
I am biased towards the YZs. Just what I am use to but also they have the best track record so far for reliability. I like my 06, but I also have the wiseco 13.5:1 piston, hotcams and WB pipe on the bike to give it the missing power it needs. Not a 450 but definately bridges that gap.
I will say that most all 05+ bikes the suspension is really good (minus the 05 KXF and 04-06RMZ which is just dated). So that is a toss up. Spend some time dialing it in on any bike and it is just great. assuming you have the right spring rate for your weight.
But the YZ is a MUCH easier aluminum frame to work on. The CRf you have to remove the rear shock to work on the carb. The YZf 06 you just remove the upper motor mounts and there is a lot of room. I personally think the KYB suspension is better, but that is a preference.