I don't think it matters a lot, as you have access to the entire resort. However, a lot will depend on your traveling party. If you have kids, you may prefer St Augustine or Bella. If you want a more laid back atmosphere, then book Key West as you will be closer to that pool that is a little quieter. Though they have started to have some daily activities and installed a new food and beverage kiosk over there. Both the Amelia and St Augustine phases have had villa renovations and I think much of Bella has been completed also. Bella doesn't have ceiling fans in the units but the small 1BR units do have ovens. This is unlike the other phases where the 1RB standard and deluxe don't have an oven. That may or may not be important to you. Key West hasn't been renovated since several years before the pandemic, but we really like the units over there. They seem to have a different vibe.
As dioxide45 mentioned, it depends what you are looking for! I personally avoid Bella as the units are quite dated and there are many complaints about units in poor condition, smell of mold etc. My favorite is Key West, as it's very tropical and a little further from all the action, but still has its own pool. Units are still quite modern.
St. Augustine is great if you have kids, and the units are very nice, but the pool can get a bit loud/crazy. If having very close access to a pool is not a priority for you, there is also Amelia, which has very similar units to St. Augustine and overlooks a lake (some people do complain of noise from I-drive, however.)