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Located just off the main drag in West End, Mariposa Lodge is a comfortable, clean and well-run hotel just a stone's throw from the beach, dive shops and restaurants. Units range from simple air-conditioned rooms to small apartments with all the amenities you'd need for a short-ish stay. Hands down, one of my favorite hotels in Honduras--the first time I stayed her, I booked 3 nights and ended up extending almost a month!
Located on a quiet residential street in downtown Cozumel, Tamarindo offers a nice variety of rooms--from simple hotel-type rooms to a thatch-roof bungalow. A couple units have en-suite kitchens--for those that don't, a full breakfast is included in the rate (plus, these guests have access to a small communal kitchen). Owned and run by a welcoming French expat.
All of the all-inclusive resorts in Punta Cana sell tickets to Dolphin Explorer on-site. If you're an indie traveler--or just want to book independently--you can reserve online: http://www.dolphinexplorer.com.do/reserve.html.
For great seafood, check out the no frills Restaurante Justicia Social. Run by the local fisherman's coop, it offers some of the freshest fish (and shrimp, oysters, octopus...you get the drift) on the island. Open until 8pm.
Olivia offers the best Mediterranean food on the island with an amazing selection of Moroccan, Greek, Bulgarian and Turkish cuisine. It's hopping most nights so consider making reservations early in the day (or better yet, the night before).
Taking a bus from Cancun International Airport to downtown Cancun is super easy, comfortable, and cheap. As you exit the terminal (no need to buy tickets inside), bear right. You'll see 'ADO' buses that leave for Cancun, Playa del Carmen and Tulum. Buses headed to Cancun leave every 30 minutes from 8am to 11pm daily. The ride takes about 25 minutes and costs approximately $4.50. There will be an agent standing beside the bus selling tickets (cash only; if you need pesos, there are ATMs inside the airport terminal). Note: Cancun buses go the main bus station in downtown Cancun; if you're headed to the Zona Hotelera--where the beachfront resorts are--you'll either have to transfer to a local bus or take a taxi (both of which are right outside the bus terminal). Happy travels!