I would choose cancer, with neurological diseases being a close 2nd. IMO, to decide this, you've got to consider 2 factors:
1) how many people worldwide are affected by it and can be affected by it?
2) is increasing life span (quantity) or making life better, but not longer more important (quality)?
#1 eliminates AIDS and malaria, since malaria only affects 3rd world, thus less people, and AIDS is about 90% preventable. most people get AIDS through sex or reused needles, so that limits the number of people who can potentially get the disease (although I'm aware a number of people are born with it from infected mothers, blood transfusions, and accidents resulting in open wounds touching, but AFAIK these are in the minority of AIDS cases). #1 also eliminates diarrhea, since supplying people drinking water will solve that, and #1 gets rid of diabetes since the majority cases of diabetes are caused by lifestyle choices, and thus preventable.
now, i'm no doctor, but i think strokes and cardiovascular diseases kinda go together, and some cases are preventable, while others aren't. still, these things can be at least healed better than the remaining 2 choices (cancer and neurological diseases).
thus, its between cancer and neurological diseases, to be decided by point #2. this is really a tossup, and part of me does think neurological diseases are most important to eliminate, but my instinct reaction is cancer, because it can kill anyone from infants to people 100+, while neurological diseases are completely reliant on age. thus, i vote cancer.
(that was a bit long winded, wasn't it?

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