We love our 2007 Honda Pilot. If you position the two carseats correctly, the middle row has a 40/60 split bench and the seats fold down easily. We have often needed to fold down the one side so we could transport long stuff like molding from Lowes. I really don't think it would be a big deal with two kids. We are having our second in September and the infant will be in the middle while the 2 year old is placed in an "outer" position. We will make sure it is set up the same way so that we can fold the 40 split side down.
Make sure you both sit in the back seat together to see what the space is like. We liked the CR-V but the vehicle width in the back was NOT good for two adults, let alone two carseats!
Looking back, I wish we had looked more closely at the Odyssey too. We did not think we wanted to go that way and while I am happy with the Pilot, I think the family might have been more comfortable in the Van.
Take lots of test drives. Ask about LATCH. Sit in the backseat together to get a feel for the car widths and spacing/feet room in the back. And LOTS OF LUCK!!
~C.
PS. We currently are (1) 2-yr old, (1) on the way and (1) boxer-lab mix!