I think that Trump's best running mate would likely be Rubio. The reason is that candidates generally pick somebody to offset things that they are seen as "weak" at. First of all, Rubio is much more recognized as "establishment." While the entire election seems to be charged as very anti-establishment, you simply cannot deny the fact that there are still a lot of believers in the status quo (which is why Hillary is still so successful even with the personality of a door knob). Rubio, while a newer politician, would still fill in the slot of being seen as both more "establishment" by being a politician and a bit more stable with his canned speeches.
Also, the general election is usually marked by a race to the middle. However, this time (given the scenario of Hillary vs. Trump) it looks more likely to be two extremists battling each other. Rubio is much more of a moderate republican which can help Trump grab some of that middle ground that will probably be really hard for any candidate to fully convince. Furthermore, with the rising Hispanic voter base Rubio will, obviously, resonate a bit better with them and maybe help to recover from some of Trumps more outrageous statements and political stances.
