I have an '06 Pilot. It wasn't what I wanted (first choice was an Odyssey, second choice any other minivan that seated eight, and those options ended up either out of my price range, or in my price range but deadly *cough*Venture*cough*) but I've discovered that I do love it. It's a lower-end model (EX?), cloth and 2WD.
As it says in my sig, I put six kids in it regularly. The only problems I've had with RF seats are putting a RF seat in both the second and third rows and being able to seat a passenger in the front, but it doesn't sound like you'll need that. With the second row all the way back, you can fit RF seats without a problem (Radian fits in the center, even with the second row partway up.) I'm not tall, but I drive with the seat bottom all the way back... it doesn't seem to slide particularly far back to me. Backrest is pretty upright, though. (I like to be as far back as I can from the wheel/airbag and still be able to safely control the vehicle.)
Car-seat wise, I'm hard pressed to find much that wouldn't fit across the second row. I regularly put a Monterey and Nautilus on the 60 portion, although it's tight. You could easily put all three of your kids (two seats plus belt) across that row. I bet you could fit Frontier, Radian, adult easily.
How often will you need to access the third row? I feel like it would be a giant pain to use all of the time, but I'm not familiar enough with the Flex to know if it would be any better. If you installed both seats on the 60 portion of the second row, and could easily fold down the 40, it might be easier, or it's not difficult to climb into the hatch, as the seat backs are fairly low in the back.
I do like how the seats stow down... I haven't used that feature much but when I first got it we picked up a friend from the airport and had tons of room for her stuff. Third row headrests have to be removed for that row to fold; second row does not. There's a nice stowage area below the cargo area for the headrests... it's designed for three, but you can easily fit a forth and I think I managed to jam a fifth in there this week
I do not have 4WD, but didn't notice too much trouble in the winter. However, I bought the car in late Feb, after an accident due to ice in early Feb, and our winter ended shortly thereafter... so what little of winter I experienced in it, I did as a VERY skittish driver. Any teeny skid was cause for alarm, lol. I don't recall being alarmed much, though.
I think the biggest reason I'd go with the Pilot over the Flex is just the reliability of the makes. I bought this car at 86k and had no concerns about it lasting me another few years. I'm not sure I would have felt the same way about a Ford, but, my experiences with them are from quite some time ago so maybe they're more reliable.