I am so sorry to leave this post hanging like this!
Here is our solution. Wire Kennel (Midwest): 
Midwest Life Stages Double-Door Folding Metal Dog... Carrier Crate (Petco): Petco Home and Travel Premium Kennel - Travel Dog Kennel from petco.com Messenger Bag (Sherpa Sport Sack): Sherpa SPORT SACK Messenger/Courier Style Small...
The Carrier Crate (with door removed) sits inside of the Wire Kennel. That leaves room for a pee pad and a water bown inside of the Wire Kennel. The Carrier Crate serves as her "den" or "bedroom" while she still has a play area where we can keep her unsupervised. She very rarely uses the pee pad, and is 99% potty trained, with the occasional accidents if we don't bring her our right after waking and 25-45 minutes after eating. Even with access to the pee pad, she still holds it all night for us (at only 4 months)! When we travel we use the Carrier Crate in the backseat strapped in to make sure she is safe in case we get in an accident. When we get to our destination(s) we walk her and then use the messenger bag.
We bought the messenger bag because it has good reviews and doesn't look like a dog carrier. We have brought her out shopping and very few people notice, and the ones that do are excited about our little girl!
We feed her Fromm dry food, mixed with wet food of various brands. We have tried Wellness, Merrick and Organics by Nature so far and she loves them! We like the ones that have food and vegetables together, and she doesn't seem too picky. We give her 1/4 cup per meal (4 times a day) and she only eats about half of that. Occasionally she will eat the whole 1/4 cup, but that is rare.
We are doing postive reinforcement (clicker) training and she is learning very quickly. She does "sit" and "down" so far, but we are still working on it. She is so smart!