I'd be inclined to take the house with walk out basement. The reason being....I've just moved into a townhouse. Originally, the daycare was to go into the basement once renovated. I changed my mind and have dedicated the main floor to the business. All the people I interviewed said how much they loved the brightness of having it on the main floor....they all said it was so inviting. With your walk out, I'm betting you've got oodles of natural light coming in, making it seem much less like a basement, yes? I don't have an issue with using the basement for the business, that's just the feedback I've gotten so far. My daycare was in the basement at my old house.

For flooring I'd go laminate with a nice shaggy area rug in cozy area (books, tv...if you have one) and a flatter area rug in main play area (blocks, etc) and nothing in lunch space. Area rugs are nice, movable for reconfiguring, easily replaced when stained....fairly non-committal.

I would probably have the parents bring the kids to the front door for exactly the reasons you mentioned. There's a really nice cabinet I bought at Ikea that I'm using for cubbies and it really doesn't look daycareish. It has empty squares for shelves and I've put fabric baskets in each. A nice lamp and stainless steel decorative bowl to hold journals, etc and it's a nice addition without looking like a kid's thing.
.

Good luck! What a nice decision to have to make