I'm sure I could rig a way to put a fiberglass or aluminum boat on top, but it would be more expensive, heavy to lift up there and take down, and harder to drag to the launching point and back. I suppose I could also get a dolly, but the boat would be more expensive than an inflatable, and the accessories (mounting equipment and dolly) would all start to add up. I'm not sure it's worth the investment for something we might use 5-10 times a year. Also, a hard boat would not be something I could use solo locally, so there is that to consider as well.
I have only started doing research, but the one friend I have spoken to who has an inflatable boat said that the inflatable is actually more sturdy than his similarly-sized aluminum boat. I think he has an intex mariner: http://www.vminnovations.com/Product_54580/Intex-Mariner-3-68373EP.html?rd=gpf_54580&utm_source=SummerSKUShopping&gclid=CIvZ9dLNusYCFdgHgQodQlUMGQ
His suggestion to me was that a kayak style boat would be more maneuverable, but that I'd have to be sure to get one that tracks well (i.e., one with a skeg, or one where a skeg could be added). And if I wanted to take extra equipment or if it was too cramped with all 3 kids, I could tow a small river raft behind, but I don't know how comfortable I'd be with that. He modified his inflatable boat to add a motor, so that tells me that it is probably a pain to paddle. LOL, just reading between the lines there.
My husband is not keen on putting anything on top of the roof. I am sure we could install a rack of some sort but he's paranoid about leaks, roof punctures, etc. Also, if we got a hard boat, he would have to be the one putting it up and taking it down (I'm pretty tough, but after my ACL/meniscus surgery, getting a heavy boat off a roof while standing on a ladder is pretty terrifying). I don't mind inflating and deflating. We already have an electric air pump for our air mattress that stays in the camper. I figure if we blow it up when we get there, we may have to add air every so often, but it should be good for a 3-4 day trip, and then deflate and put it away.
How is the 2 person sea eagle as far as paddling solo? I've taken my daughter out in a tandem hardside kayak and it was a bear to paddle. It got a little easier when I took her paddle away (she was inadvertently working against me and splashing me in the face!) but it was still tough. It had a lot of drag and didn't track well. Does the Sea Eagle come with skegs?