Science Funding
The current congress has the highest percentage of science illiterate members than previous years. There is one on the science and technology committee that has stated that he believes the world to be 9000 years old, that evolution and the big bang theories are straight from hell.
As YetAnotherBob stated, congress controls the budget while the president can suggest and negotiate budget proposals. The only other control the president has is veto over a bill and send it back to congress to rework or pass with veto proof support.
Science funding for NASA the US Weather Service NOAA and other beneficial agencies will probably be cut regardless who wins the presidency. Neither party is capable of leading the US into the future while they bicker over the past and are cavalier about the present.