I travel to this area for work regularly. Off season, I prefer to stay at the Boca Beach Club, as it it light years nicer and service is much better than the Boca Resort. During "season" the room rates get to be a bit much for my T&E budget ($400+ per night), so I usually stay at the Hilton Suites in Boca (also a nice place with a very good restaurant called City Fish Company next door). The Hilton Suites is about 10 minutes west of the beach though.
My first, and only, experience at the Boca Resort was not good. They did not upgrade my room and I was stuck in the old "cloister" section of the main building. When I asked about my room upgrade they gave me excuse that the hotel was full (although it did not appear to be crowded and in the morning, the rooms on either side of me did not have newspapers out at 6:00 am, as mine did). They do participate in the points program. The resort fee in my opinion is just a way of getting some extra $$$ from you,as it is supposed to include some tips, but the bell staff still expects tips (you can tell this from the way they stand and wait). The parking is overpriced and takes forever to get your car (I waited 15 minutes for my car and the drive area was not busy). All in all, my room was very old and worn with the gold fixutres actually pitting. I wouldn't go back unless I could be assured of staying in another section of the hotel.
On the other hand, the sister property, the Boca Beach Club is stunning. The rooms are very modern and chic. The hotel has a "south beach" feel upon walking in. The beach is nice, the service is good, the only negative is that the choices for dining are quite limited. You almost have to take the shuttle to the Boca Resort to have variety in dining choices. Given that the room rates are usually similar, I would pick the Boca Beach Club. Off season you can usually find a AAA or MVP rate under $200. I am still a bit bothered by the resort fee and the high parking charges though (personally, I would rather just have them include both in the room rate). I have always received upgrades to Beach View rooms with great views. The valet service here is much better than the resort (it only takes 3-4 minutes to get your car). I have stayed here about 5 times in the past year and continue to choose this hotel while in Boca during the off season...