if they decide to pull the plug on certain projects, those projects are going to have a very tough time.

That looks like a problem to me.

Also, I'm not sure how the whole system works, but let's say I'm a medical researcher. I may be tempted to focus on researches that get money easier (e.g. what gets funded easier by the Gates foundation), instead of focusing on something else (e.g. cancer research). Suddenly the Gates foundation dictates the trends.

That's really some simple thinking here but seems like a valid point to me. Still, I could be totally wrong. I'm not a medical researcher.