I think both Mission Bay and South Beach have compelling arguments, the main difference I feel is Mission Bay will take 20 years to fulfill its potential, wheras South Beach is basically infilling.
Really you can't answer this question without understanding the question first. I can tell you what I like, but that's really moot to you. Define your goals and make a plan to get them. Good luck, and have some fun. San Francisco is a great town.
Mission Bay, you really only have Berry St in my opinion and over there you have 255 Berry, 235 Berry, Arterra, Park Terrace.... 4th and King/Townsend is a very CONVENIENT location for public transportation and everyday shopping (Safeway, Borders, Walgreens all nearby), 3rd and King/Townsend is also bustling and convenient too in Mission Bay but not exactly quiet and can get busy during ball games - so I do not know what you mean by GOOD LOCATION - do you mean, active, alive? Do you mean, quiet/serene? What do you mean by good location?
Other locations in South Beach that are "good" are the intersections of Main and Folsom - 1 block from the Embarcadero and waterfront - The Infinity (my personal favorite!) is located right there as well as 300 Beale (Embarcadero Lofts) nearby as well as 75 Folsom St. Honorable mention for great locations in South Beach would include the area around South Park on 2nd St.
Quality buildings I think you have to start with The Brannan, hands down the best built/quality building in this area. The Infinity is good too - 200 Brannan, 300 Beale St (Embarcadero Lofts) is a quality loft conversion building, Watermark is considered to be a building of reasonable quality too - 301 Bryant is also highly regarded. There are just so many good buildings to be honest.
HOA fees - I assume you don't just mean, HIGH HOA fees, but HOA fees that are a good value, The Infinity gives good value for the HOA fees I think for a full service / full amenity building. If you are looking for low HOA fees then you should turn towards some buildings on Berry St in Mission Bay like 235 Berry and 255 Berry for example.
There is so much variety between all the buildings that it's wonderfully confusing! I love community and neighborliness, with the dog friendly buildings as well as the age-mixed buildings; making one of my favs the Towers at 88 King; it has a diverse and close knit community and lots of protected sun on its pool ... people love living there; the Bridgeview has good neighbors who love dogs. The pool at The Brannan is too exposed to the wind -- I'm a weather wimp! I like the Portside pool; and the Bay Crest is a little too corporate rental atmosphere for me. Mission bay buildings have such a different feel than South Beach ... I'm looking forward to a tour of the Esprit Park complex, personally, and looking forward to other comments on buildings from Trulia experts!
The Palms may be a good deal price-wise but take a look at the construction and the feel for the building in general. I would be glad to go into greater detail.....or see my answer below.
You need to consider what the inside of the building is like including the hallways and general feel of the complex. I feel there are other complexes in South Beach and Mission Bay that are better, have nicer space and would make a better resale in the future. I am just giving you my opinion as a realtor who sells in the area....and obviously others (see below) disagree with me.
There's a new loft building open on South Park -- has anyone toured it yet? I certainly enjoy the diversity of opinions here!
I will have to give condotessa a thumbs up on that answer. The Palms seem to be one of the better deals in the area. You might not want to buy new if you're looking for the best deal however. You can probably pick a couple of them up that have only been lived in a short period of time. Also there are some good prices and a better location, in my opinion, on the corner of 4th and townsend. Give New City Homes a call or contact me for more info. As far as worst buildings... you looking for something to use as a fixer upper?
Normally I would not contradict someone's comments but I would skip the Palms. The units can be noisy as it is right on the freeway and the long hallways give it a hotel feel. I would look to buildings like Embarcadero Lofts, The Brannan, 200 Brannan, all the buildings on Berry Street, Oriental Warehouse and so many more. I would be happy to give you my opinion on the new construction like Infinity, One Rincon Hill, etc. Please contact me if you wish to pursue this further, Otherwise, good luck in your search!