All I can do is tell you what we have decided. in the past with a 3 year old and then a 4 year old, we have stayed off site for 10 days and on site for 4 days, giving us the best of both worlds.
however, on our next trip with a 3 month old and a 6 year old, we have decided to stay offsite for the entire trip. A number of reasons, first off all I didn't fancy moving anywhere with all the gear that we are likely to be carrying with us, on our last 2 trips we lost about 1/2 day on the move day. Since we stay for 2 weeks, that's not too big a problem, but it is still hassle we can do without.
Also, I think for us the kitchen, laundry and 2nd bedroom will be a huge bonus. It means that my older dd can go to bed at a reasonable time some nights (we don't stick to normal bedtimes on vacation, but sometimes it's nice to put her to bed and have some adult time), and we won't all be tiptoeing around in the dark. Also, no hassle preparing food for her or baby - I have warmed bottles for dd1 in the coffee maker before, and yes it's doable, but there are easier ways!
Something to bear in mind though , is that we will hire a car regardless of if we are on site or off site, and even when on-site we tend to drive to the parks, we just find it easier with strollers and all the bags etc to drive ourselves, so the onsite advantage of transportation is not a big one for us. Also, we don't do mid-day breaks, instead we do shorter days, but more of them.
That's what works for us, but I am sure others will tell you you can't beat a monorail hotel (of course, I can't afford a monorail hotel!)
Bev