I'm looking for the places that a world-diver must dive.
I am Galapagos x5, Cocos x1 (10 days), Malpelo x1 (9 days) - all liveaboard trips but I have also dived Galapagos land-based out of Santa Cruz, San Cristobel and Isabela. The rest of my dive experience is in my profile.
"Must dive" is very subjective but personally I would not put Fernando de Noronha or Malpelo on "must dive" lists. Do some digging on Fernando de Noronha and I think you will find topside it is very beautiful, but the diving is not exceptional. I was researching it within the past year both online and via divers and my bar wasn't even as high as "must dive". If you're already there of course why not - but that wasn't your question.
I would put Galapagos and Cocos diving significantly above Malpelo diving. The Malpelo land visit is outstanding, but very few people on the liveaboard I was on managed it physically, despite their interest. In my experience, Malpelo diving is very hit and miss. Again if you research, I think you will find this consistent with many people's experiences -- of course luck always plays a role. In the area already and offered an incredible last-minute deal? Again, why not.
Have you budgeted for a Galapagos liveaboard? I would happily sacrifice diving in several areas in order to dive Galapagos by liveaboard. Land-based Galapagos can be very good, but Darwin and Wolf are blow your mind spectacular.
Bonaire I found interesting as an experience (pop tanks in the truck and run your own dives). It's Caribbean diving, but arguably worth doing for the overall experience if you don't often do 100% self-directed diving. If you do make it to BON, Bas Tol's Lac Cai night dive is a must do.
You might look into cold water Argentine diving. I dove with someone who recounted a couple very chilly dives that I would have signed up for were I in the area - I can't remember exactly where, and the wildlife as I remember his report wasn't dense, but it was interesting.
I would also probably dive Easter Island were I close by, against my better judgement. There's an informative trip report on ScubaBoard if you look for it.
Too bad you're not doing Costa Rica. Bat Islands land-based is worth doing.
Would be interested to hear how your dives went when you return.