It's not really so terrible.... but I always breathe a sigh of relief when I finally step into my hotel room !!
My favorite airline to Puerto Vallarta is definitely Alaska Airlines. They are usually on time, and have many direct flights that arrive at a convenient hour. Also, Alaska seems to have frequent sales.... and my airfare has ranged from $202 to $588 for a round-trip flight in coach. I usually book several months in advance if I know what dates I will be travelling. Yes, a cheaper airfare COULD come up, but the price could go higher just as easily.
When we arrive in Puerto Vallarta at the Gustavo Diaz Ordaz International Airport, the plane does not normally taxi up to the building. Instead, it stops a little way out and a bus is sent to transport passengers from the plane to the terminal. (It may... or may not..... be air-conditioned.) After passports are checked, it is a long walk to the baggage claim area. Then you must proceed through customs. Ahead of you is something that looks like a small traffic light..... if you press the button and it turns green (this happens most of the time) you walk through customs and out the door. If it turns red your baggage will be inspected and you will have a short delay.
As soon as you clear customs you will be besieged by many people all talking at once. Do your best to ignore them !! They are condo salesmen. If you have arranged transportation to your hotel on the Internet, they will even lie to you about being your driver. Proceed to the main area of the terminal and you should see your transportation person holding a sign up with your name on it. If you did not arrange transportation there are taxis and vans outside, and you may buy a ticket inside at a booth near the exit door. They are regulated as to the lowest fare they can charge. They charge per person for these taxis, unlike the taxis in town. Be prepared to pay quite a bit to get to your hotel, but this is the only transportation that is priced so high.
Once you have unpacked at your hotel, you may wish to venture outside... or to the grocery store if you have a condo. You may take a taxi for less than $5, or you may walk, or take the local bus for about 60c (as of Jan-2013). I usually take the bus or walk to the store, and hire a taxi for the ride back if I have several bags. Many drivers speak English. IMPORTANT: BE SURE to settle on the price BEFORE you get into any taxi !! Taxis are very reasonable in town, but will charge more at night when the buses stop running around 10:00 pm. In early 2008 I paid $4 US for a fairly long taxi ride. ($6 US in 2013) You are not expected to tip taxi drivers.... the local people don't... but you may if you wish.
It is easy to get around by bus in Puerto Vallarta. They write destinations on the windshield in big white letters.... for example: Hoteles. Buses do not stop on the Malecon, but will stop near the 2 bridges in Old Town at the south end of the Malecon. If you are travelling north, Woolworth's is a good place to catch the bus. It is 2 blocks east of the northern end of the Malecon.... turn up at MacDonald's.
If you would like to visit Guadalajara or Mexico City from here, I strongly urge you to choose the ETN Line. These are luxury buses with only 24 roomy, reclining seats per bus. I think it is the only line to serve you a welcome lunch. The 2 bathrooms are very roomy, and tea and coffee is available at the back of the bus during the trip. The bus is air-conditioned, has plasma TV screens, foot rests, and a controlled speed limit (governor). I rode this bus to Guadalajara-- the trip took about 4 hours, and was very relaxing ! I paid about $40 US. We arrived at an enormous bus terminal in Guadalajara, and one of the many waiting taxis took us to our hotel with no problems (about $10 for a 30 minute ride).
Another option would be to fly to Guadalajara from the U.S., and then take this bus to Puerto Vallarta. The bus system in Mexico is excellent.... DON'T be afraid to ride the buses !!
Note: As of Jan 2013 Guadalajara and Puerto Vallarta are considered 2 of the 3 safest cities for tourists in Mexico.... and Cancun is the third. I believe they are referring mainly to violent crimes. I feel Puerto Vallarta is VERY safe at this time, and would travel there alone! I think the other 2 cities have more petty crime and muggings.