Finally a question I can answer properly! 
Drew, Los Roques is kind of the same, I love Los Roques because is really seclude and pristine. Canaima and the Angel falls is really sweet to visit, but be aware you are going into a jungle style trip with all the bugs and discomfort included. A different approach to Canaima National Park is “La Gran Sabana” (The great plains), really cool stuff there, waterfalls and nice sights and plains (you can get a chopper ride here, is awesome!)
http://www.google.co.ve/images?hl=es&q...360&bih=578
“Morrocoy National Park” is a series of keys 4 hours from Caracas, so that may be worth it to visit, but is not a big deal… I concur with Luiz about diving Los Roques, is the same as Bonaire but plenty more fauna.
Margarita is a must if you pick a nice hotel near the nicest beaches. Rent a car here is a must, go with Hertz or any other rental, familiar to you. “El Yaque” beach is the sweetest place for kiting, and also is the only one with proper stores for rentals and related stuff. BTW I´m not a big fan of Margarita diving and specially “Los Frailes” diving as Luiz is. Neither the neighbor islands Coche and Cubagua.
Of course I am biased, but you can ask Jean Bruneau (Aquatica) what he think about places to visit, I took him for several places (diving ones) a couple of years ago, and he had visited Venezuela a few times.
If you need a ride or a safe drive trough Caracas, I´ll be more than happy to take you guys out anytime you like. Also if you want to try local cuisine or fancy a nice gourmet / fusion cuisine.
In my opinion, this could be your tourist list:
-Los Roques (with a nice accommodation) try this ones: http://www.macanaolodge.com/ or http://www.posadaacuarela.com/
-4 days Canaima trip (Salto Angel)
-7 days Canaima trip (La Gran Sabana) I recommend combining this two…
- Margarita (with a nice hotel) Check it out Chana´s (One of my favorites) http://www.chanahoteles.com/galeria/?modgal=suitgal
- Morrocoy National Park
-Puerto Ayacucho (“Venezuelan - Amazonian/Indian town”) In this town recently opens a restaurant where the chef includes tarantula, and many bugs including red ants in their menu!! So cool…
- Mérida (City) Kind of cold weather mountain city, for romantic walks with the gf …
I think with 10 to 14 days between margarita and one other pick, you are set. If I were you, I probably visit Canaima's Angel falls and “La Gran Sabana” as a package, and expend a couple of days in Los Roques.
There are several tips you must know, including exchange of currency (this can be very tricky and you can get scam), so through me an email (rodriguezfelix1@hotmail.com) every time you need to know something. I´ll be pleased to help you planning your trip.