At first, pick John Kasich as VP. These two are the best running mates the GOP can offer this year (although I prefer Kasich as prez and Rubio as VP). Second, present himself as a fresh alternative to Hillary, who represents the past and the establishment.
This here might be a path for Rubio to capture the presidency. I think WI is a little more likely to flip to the GOP than PA. Both are Close, within 1%, in that scenario:
Senator Marco Rubio (R-FL)/Governor John Kasich (R-OH): 278 EV. (49.9%)Former Secretary of State Hillary Clinton (D-NY)/HUD Secretary Julian Castro (D-TX): 260 EV. (48.9%)With toss-ups:227-
191-120