FWIW, I have done a week in Cozumel twice, and both times I arranged everything myself.
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Airfares:
Both times I traveled it was $150 - $200 cheaper to fly into Cancun, so I opted for the Bus-Ferry-Taxi routine to get to my hotel on the island. It adds about 1.5 - 2 hours to the total travel time, but it gave me more flexibility on arrival and departure times.
However, once while researching a trip that I did not take, the flights direct to Cozumel were cheaper on the particular dates that I was checking. Go figure. It is always worth checking.
I use CheapTickets.com, and they allow you to specifiy an airport, but to also check other airports within 80 miles, and that will cover both.
I live in San Jose California, so none of the FunJet things seem to work for me. I keep hearing about the great prices from Houston and Chicago, but I can never seem to find a deal as good from here. I guess I just need to keep going back until I get it "right".
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Air-Land-Sea (Fly - Bus - Ferry - Taxi)
The air-land-sea route doesn't work for everyone. Both times I enjoyed the trip. The Bus was airconditioned, and the movies were subtitled, so it got me started on getting into the spanish language culture. My only complaints were that the curtains were closed (to keep it dark for the TV) so I didn't see much out the windows, and that the trip was not long enough to see the end of the movie!
The buses departed the airport at X.45 each hour, so I only had a brief wait (pure luck) each time. Walking the guantlet to get to the buses was not swell, but it was good practice for the area around the square in Cozumel (if you know what I mean - if not, you will)
The first time I did the trip I ended up on the slow diesel ferry with bad fumes. I believe it was the blue and yellow UltraMar ferry. I have always used the WaterJet since then, and it has been fine. (on the last trip, the UltraMar seemed just as fast, so it may be just one of their ships that was sub-par; not sure) YMMV.
There is a line of Taxis waiting for people unloading from the ferry. On my first visit, I got a petite young female taxi driver that couldn't heft my dive bag into the back of the cab, and she did not know where the hotel was, even after I told her and then showed her the address. Now that I understand the layout of the island, I cannot imagine why she had trouble. Doh!
One word of warning on Taxis, and I have read it here other times: Agree on a price, before you get in the cab. Once you are at your destination, you have a lot less negotiating power. Julie was awesome: Cabbie said 50, she said 30. Cabbie said 50, she handed him 30, and climbed in. Cabbie shrugged and got in and drove. (she had paid 30 before, so she knew it was reasonable)
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Hotel:
I have stayed at the Hotel Flamingo on both occasions. I went there the first time because I was meeting some people there. Bob had stayed there numerous times, so that was where we stayed. It was $39 a night off-season for a room with 2 double (Queen?) beds, regardless of the number of people. (That price can be found on their website with a little searching - remember that you are diving; they don't ask who you are diving with)
The Hotel itself is small, with about a dozen rooms. The owner is an american from the SF Bay Area. The water pressure is not great, and you sometimes have to wait a while for hot water, but I think that is fairly normal for many parts of town. There is no elevator, so the third floor is a pain. I prefer the second floor, and I always ask for a room with a Fridge!
They offer meals at the Hotel, and it was very good. It is not a big restaurant, but they will cook up meals for you on the spot. We have eaten breakfast and dinner there several times, and it was always very good. At lunch they will get the people from the place across the road to come over to take your order and to deliver food etc.
The part I liked the best was that I could walk to virtually everything. The Hotel is on Calle 6, so it is just a few blocks north of town, and less than a block from the water. There are a couple little "convenience stores" between the town center and the Hotel where I have bought water, ice cream, cookies, etc. It is a 5 minute walk (or less) to anything in the main town area; Casa Denis, Prima's etc. It is 3 minutes to Guido's or Cinco Soles (Pancho's). We did walk down to the TGI Friday's area once, but I preferred the older parts of town.
It was about 5-7 minutes to the dive shop each day, and then 2 minutes from the dive shop to the pier. I thought it was great. My buddy didn't like the walking, but he could have taken a cab! We looked at some other hotels closer to town, and might try something different the next time. (I would use Hotel Flamingo again in a heartbeat, but my buddy wanted something closer)
After a morning dive, I always wanted to stop and eat at one of the "economicas" in the vicinity, then return to the hotel to get cleaned up and get some rest. It works great in my opinion. To each his own.
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If Chuck can share how he does it all for $100 a day, I am interested in learning.
On my first trip (2003) I think that I spent around $1500 for everything for a week; about $550 for airfare, $360 for diving, $300 for Hotel, plus food and tips and lots of souvenirs.
On my second trip (2004) it was about the same because I split the room cost with my buddy, and I didn't buy so many souvenirs, but I did an extra 2 tank dive to Barracuda.
(I have the actual numbers at home)
Just some opinions for reference.
Wristshot