The difference between a Villa and Manor is size, a Villa is 384 square meters and the Manor is 672 square meters.
If you choose to upgrade, you would still keep the pet and gain a Design Experience from the pledge (hairstyle, tattoo, and consumable item) of your choice though you can only pick one from the list. It would be worth the upgrade for the Design Experience alone.
The phoenix is a reward to people who pledged during Kickstarter or during the store opening last year. The tiers changed after Dec. 27th so the Phoenix isn't available now from the store.