Congrats on getting engaged!
Concerning transportations, you may want to look for a hotel that includes transportation to and from the airport. We are getting married at Dreams in Puerto Vallarta and it is a little outside the city and transportation to and from the hotel in included in the room fee, which is a nice bonus.
Also you may lean more towards the all-inclusive if your guests are tending to be more cost aware. Because even though the room rate may be a little higher, all food and drinks and some activities are included. Whereas if you go out to eat every night it can add up really quickly, especially once drinks are included. Because remember going to a foreign country people are less likely to go and explore for a more cost concious place to eat and instead look to the touristy areas where they feel safe and tend to be more expensive. I know that all of our guests so far have been impressed with how "inexpensive" coming to our wedding is.
I totally recommend going with a TA though, they will help guide you through EVERYTHING!! They will give you options and then work with you and your guests in order to get the cheapest options available. My TA is a lifesaver and got us two roundtrip tickets to PV at the times we wanted for under $700. And I know for a fact that by booking through a TA you get way better pricing, the hotel wanted $2250 for a 5 night stay + flight at our resort, whereas our TA got my FI's mom the same package for a total of $1850.
Just make sure you are not only happy with the resort but also with the wedding packages offered at the resort. And keep in mind that if you get married at an all-inclusive and some guests choose to stay at another hotel you/or them will have to pay a guest fee for the day of the wedding that can range up to $80 per guest. Because all-inclusives are very protective of who they let in since all food and drinks are included. We let our guests know that ahead of time, so if they choose to stay somewhere else they know they will have to pay the fee themselves.
Also you can orchestrate your wedding to how you like, just work with your TA and the hotel wedding coordinator. A hotel that I really liked and offered great packages for smaller wedding parties (which didn't work out for me) and is more of a "small town feel" without the price tag is Isla Mujeres Palace. And a nice thing about the Palace Resorts is you stay at one, but you play at all of them. So Isla Mujeres is an island off Cancun, so you stay on the island but can take the ferry back and forth to Cancun and go to the Palace resorts there to enjoy their restaurants and beaches as well.
Palace Resorts - Welcome to the Official Site - Isla Mujeres Palace
Hope this helps!!