Re: Species impact
Great questions.
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But regarding #2 again, there might not be a dominant disease causing virus or bacteria that holds humans back from a greater impact, but rather a group that collectively does so, or which alternate over time.
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This is why I picked malaria/mosquito. It definitely is an obstacle to human civilization and, more importantly for this debate, is located in a certain place (say, the tropics) of really high biodiversity and can "protect" that area. While other diseases may kill more humans at certain times (influenza, plague, etc.) they don't have the effect or localization malaria has. That's also why I don't think rats are as good of a choice as the mosquito vector, they're pretty much everywhere and while they can have on effect on controlling human density, I don't think they have nearly as much effect. I did see something in Discover and other places on them wiping out species that I thought was interesting.
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However as 3/4 of the planet is covered in oceans, something aquatic like algae also has to be considered.
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Yeah, here's where the species question comes in. As groups of species, a lot of other organisms have a greater effect than humans (like algae). Maybe we could go to the genus level (still be in the letter of the OP since we are the only extant species in our genus)
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It is also worth noting, that many predator species that would otherwise be candidates for the original question, are held in check if not extincted by humans,
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But predators are often affecting small local populations (as opposed to tropical diseases - which have a much larger area).
I think that the rat would definitely drop down the list if humans went extinct.
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