Deciding whether to take the bus or car is really about personal preference.
Probably a car would get you to the parking lot faster, but then you have to find a spot, and WALK back to your car when you leave. If you go all over DTD that can be a considerable distance from where you end up, as DTD is quite sprawling.
If you take the bus, sure you have to wait for the bus, but it drops you off in a central location,and you can pick it up there too. Actually there are two stops - one in the middle of DTD, and one at the far end of the Marketplace. If you can get dropped off at the Marketplace end and start your visit there, that's probably better. They only use that drop during certain hours though.
The other pluses of the bus are that you don't have to designate a driver - if someone wants alcohol, and you don't have to navigate around WDW. EVeryone gets to simply ride.
The distance from your resort to DTD will vary considerably depending in which resort you are staying at, and what time of day you go. This will also affect how many stops your bus will make. If you have to loop around CBR it might be faster to drive. If you are coming directly from PORFQ - you will take a ratehr pleasant short boat ride to DTD.
The Boutique is located at the back of the WoD store. It would be a shame to miss the entire store just to avoid the Boutique area. It is pretty easy to walk right past it anyhow. Also, if you intend to get you younger daughter anything princess, that store is any young girl's paradise! They have tons of costumes, hats, stuffed animals, hair ribbons, toys, etc. the store has a number of other sections too. It's also a great place to find stuff for folks back home, and the far side has a great pirate theme for the boys.
Our favorite dining at DTD is Wolfgang Puck's Express. You can sit outside and the food is great. We've loved everythign we've had there, especially for the price.
We were quite disappointed with the Wolfgang Puck Cafe though. So not worht the extra money.
HoB was good, but has strictly Southern food. Good, but a little limited.
We looked at Raglan Road, but the overpowering smell of grease deterred us. Not that I dislike fish and chips.
Bongos was neat. The decor, including the bathrooms, is very nice. The food is Cuban, so it's exotic and might not be to everyone's liking.
If you've never been to a Rainforest Cafe, it's fun to check ti out. the food's not the best, but the theming is really fun. Even if you just wander through the giftshop.
You can also take a boat shuttle to either Saratoga Springs or POR. You could even eat there. If you just want a break from the noise or a way to settle down the little one, this might be just the thing. Also, the resorts are usually pretty quiet mid-day.
As for stores, in addition to the ones people mentioned already...there's a Disney pet store that's really cute if you have pets. At the back of the Chritmas store they will personalize lots of stuff. They have laser embroidery and engraving, and I they do other stuff in the store sometimes - like painting ornaments.
There's also a store that only has stuff under ten dollars. It's basically stuff you can find elsewhere, and some seasonal clearance items, but it can be a fun little place to let the kids loose.