A good way of deciding where to stay in town would be to know beforehand what interests you and if the zone you are going to stay in has them too, it's hard to give a detailed recount of everything a specific zone has, but we'll try to include the highlights.
The north zone is quite extense, starting in the south at Bucerías and ending on the NW side of the bay in Punta Mita, you'll find small towns that have a more Mexican feel to them, meaning less developed, a bit more rustic, more traditional, say, the-neighbor-has-chicken-and-roosters-in-his-backyard traditional, and when you pass La Cruz you start finding more resorts, some very exclusive and luxurious, like the St. Regis or the Four Seasons in Punta Mita. In general, the north zone is more for people that want to relax and get away from it all, no night in town, no boozing and so on, either older couples, romantic couples or families with pre-teen kids.
Bucerías is the largest town in this area, many travelers swear it's what Puerto Vallarta was like 50 years ago, it's still very active, has a great long and wide beach, many water related activities, for example the area is a kitesurfing, windsurfing favorite. There are good local restaurants and even international ones too. Beyond the bars, small shops and the beach side restaurants there isn't too much to do.
Further north you arrive in La Cruz de Huanacaxtle, a smaller town, that has changed its profile quite a bit since the Riviera Nayarit Marina was installed there, there are a number of great little restaurants, the local beach, La Manzanilla is very good too.
Between La Cruz and Punta Mita there are only a few condo developments and some nice beaches, like Destiladeras.
Punta Mita is also a small town, with its plaza and church, the main drag is El Anclote beach, here you'll find some great restaurants and the chance to enjoy sea and beach activities. Boats can be rented to visit the Marieta Islands too or to go out scuba and snorkeling.
This area is a purpose built tourist destination, á la Cancun, so there is no downtown, no church, no city square, just hotels, resorts, golf courses, two marinas, condos, villas and a few malls and other services that have opened to cover the needs of the local inhabitants and the visitors.
This area is more for the all-inclusive fans, where you mostly stay in the resort, get a tan, relax and eat-drink to your heart's desire.
There's always the chance to jump into Puerto Vallarta or Bucerías, but it'll be a once or twice happening as it's a bit of a distance, specially if you want to save and take a bus.
The beach in Nuevo Vallarta is very nice, wide and great sand and the waves are not too rough, so it's also recommended for families with pre-teen kids, even with teen kids that are not too rowdy, there's a lot to do here too, and the malls that are close by will help them get something else done than just sit in front of their portable "cuckoo" machines (you know, iPads, Nintendo DS's and so on).
Now we are in Puerto Vallarta, though the Marina is not walking distance from downtown Puerto Vallarta, it's close enough and well connected that you won't hesitate so much in grabbing a taxi or a local bus to go there.
There's a marina with stores, restaurants, cafes and bars that should cover most of your needs, there was once a mall, but it didn't catch on and has been left abandoned... wonder for how long. There's a championship golf course too and many condominiums and a number of the best hotels and resorts in PV. Most, if not all are all-inclusives and the beachfront ones have a good beach to offer on the Pacific side, it's not nearly as good as the ones in Nuevo Vallarta or further north, the sand is a bit grey, making it hotter and not as esthetically attractive.
Many of the hotels open their doors to the spring breakers, so the Marina area is definitively a place with a bit more noise, more "action" that caters more to a variety of clients. You'll find the very luxy hotels, like the CasaMagna Marriott or Casa Velas more for the older crowd or the Velas Vallarta and Meliá, more for the younger couples, some with kids.
Besides the Marina and the boats you can take from here into the bay, this area doesn't have much more to offer than food, hotels and the golf course.
The hotel zone starts off around the harbor area, where you'll find the cruise ships and the Galería Mall beside the local Walmart and SAM's Club. There are many hotels in this area, from the most humble two stars up to luxy 5 star hotel/resorts.
Pitillal is close by, if you are interested in learning how real Mexicans live, a small town with its plaza, that has been overun by PV's growth.
There are quite a few malls in this area, so you'll have access to banks, food, restaurants, movies and much more. The area in general is relatively new, so there's not much to enjoy in terms of architecture and history. Distances into downtown are now possible on foot.
There are a few important nightlife options in the area, as well as some of the top restaurants too, so you are not far from it all.
The beaches in this zone are not much to write home about, if there is any, they are normally small, crowded and barely more than a bit of sand before reaching the containing walls of the seaside hotels. Some, like the beach by the Sheraton are nothing more than seaside edges full of 3 inch rounded stones...
This is the historical part of town, despite the name given to the area south of downtown Puerto Vallarta, this is the real Old Vallarta, here's the plaza, the iconic parish, the hills and the Gringo Gulch. It's in this part of town you'll find the Malecon, a boardwalk that is the starting point of most the area's activity. If you are into strolling around, shopping, people watching, eating, dancing, art, bars, cafés, history, architecture, then this is the zone you need to stay in together with the Romantic zone.
This area offers less than a handful of all-inclusive resorts, in part because the space is limited, and mostly because it makes no sense, having an incredible array of options right outside the door, who would stay inside the hotel for meals!
The only decent beach in the downtown area is Camarones Beach north of Hotel Rosita all the way to Villa Premiere, a 700 yard beach, but Los Muertos Beach and Olas Altas in the Romantic zone are within walking distance too.
Main attractions: the Malecon, the Guadalupe Parish, the plaza and amphitheater, the hills and Gringo Gulch, Isla Río Cuale and the bridge from Gringo Gulch to the island, the various Flea markets, the Naval Museum , the side streets.
Even though the romantic zone is a part of town that is actually newer than the downtown area, it's also an area that developed primarily around the first hotels and bars on Los Muertos beach, so it's more geared for tourism, lots of stores, restaurants, cafés, bars, clubs, all one beside the other, so this place is electric with activity, but it's also a bit less attractive from the architectural and historical point of view. Even so Olas Altas and Los Muertos beach all make up for it and more. The malecon on the north side has now been united to the south side by the Malecon II and the pedestrian bridge over the Cuale river, so it's almost as if it all was just one long beachside stroll.
Old Vallarta is a favorite of the expats and the regulars in town, this is because there's always something to do, always somewhere to go and enjoy their town. It's a great option for families with kids of all ages, great for the older couples and it's the best place for the LGBT crowd, as the south side of Los Muertos offers many of the resorts they favor.
Main attractions: Los Muertos beach, the pier, Olas Altas, the Isla Cuale and the Farmer's Market (Nov.-May).
Want to be in the middle of it all, here and downtown are the places to stay.
The South zone is a bit like the North zone, it's a bit far from it all, transport helps you come into town, but it's not something you'll do so often, so you tend to stay in the resorts and hotels. There are some very exclusive condo developments in this area too.