Hi, I believe the OP is the dad that wants to take his 6 yo daughter. Mom will be home with the 3 yo, right? I say go for it. The 3 yo will be happy to have Mom all to himself. I bet Mom can plan some fun things for him.
I alternate trips between taking my 6 yo DGS and taking my teenager due to her school schedule. I have taken two trips alone with DGS when he was 5 and 6. We have some very special memories of these trips and there are plenty of opportunities for bonding in WDW, IMO.
As far as where to stay, I would go with what you can afford or what you want to spend. Since you are staying near Epcot in Sept, maybe you could stay near MK at a monorail resort, if money is not a concern. We have stayed at Poly and Pop and both were great choices imo, it's all about what you would like to spend. A monorail resort is a great choice, but with a heavy price tag. Lately, I have decided I would rather save money and not stay deluxe unless I had very small children. In my experience, Pop and the Mods are great.
And you're right. Before you leave, you must accept the idea that you cannot ride many of the adult rides, depending on your daughter's daredevil level. I wouldn't try to convince her to go on rides she doesn't want to go on, even if you think she can handle it. It's easy to get caught up in the moment at WDW and try to "get your moneys worth," but a child getting scared on just one ride may cause her to not want to ride anything, including tame rides like Dumbo, even if she has already gone on it with no problems.
As DGS got older it was a little more difficult not to be able to enjoy attractions I thought he could handle, like Goofy's Barnstormers, but I didn't want to force him. One year, we didn't get to ride Pirates of Caribb. because he was a little frightened on it the previous year when he was 4. Needless to say it was hard to accept being at WDW and not riding Pirates, but these are the things you have to accept without making the child feel bad that you are unable to ride because they won't go on it. It can turn a good trip into a bad one in a hurry. Haven't we all seen adults forcing kids onto rides, the kids are screaming, and everyone else around them has a miserable riding experience? Sorry, I hope I'm not coming off as preachy, but you asked for tips, advice, and suggestions.
I think you will get a better handle on your decision whether to go in Feb or not, after your Sept trip. Good luck and have fun at YC. We have stayed there and loved it. The outdoors area at night is so fun and festive.
Tink