Manchester Hyatt downtown is a great place to spend a few nights. Also best location to start at - only 5 minute Uber from San Diego airport. An alternative option downtown is the Andaz. Both in prime locations.

I'd avoid Indian Wells unless you want to play golf, tennis or sit by the pool all day.

The Park Hyatt Aviara is a beautiful property and the most high end of those you listed. You could easily spend 2 days here and take a short drive down to the local beaches.

If you have the energy to make a 3rd stop for 2 nights, the Huntington Beach location is also nice and very different from Manchester and Aviara. It is right on the beach in HB and close to the pier. 2 days is plenty of time to spend in HB -- I'd recommend making the short trip to Newport Beach and Laguna Beach.

If I were you...

Start: 4 days at Manchester Hyatt -- enjoy downtown, seaport village and all that San Diego has to offer.

2nd stop: Make the drive to HB. Spend 2 days and try to make a day trip to Newport and Laguna as well.

Final stop: 2 days at Park Hyatt. This will position you in north county SD before you leave (assuming you are flying out of SD).

Let me know if you have specific questions.