...I would think that methane/oxygen would be significantly easier to store in space...



This strikes me as the most important issue.It is seldom discussed, but the launch windows for flights to Mars only occur every two years. Building a special rocket (with related infrastructure) which only launches once or twice every two years will be impractical, no matter what that rocket is.So when the rocket is re-usable, each Mars mission should be broken down into multiple smaller launches, which will sit in Earth orbit (for many months) until the departure window opens. As Roy says, H2 is terrible for long term storage of an Earth-departure-stage, even kerosene/oxygen has the problem of kerosene freezing at LOx temperatures, but methane/oxygen seems ok, and will be much cheaper than the hypergolic Super Draco fuel (used in the Dragon capsule).The other trick to make a viable Mars rocket is to use a multi-core version of a rocket that is designed to serve the Earth orbit market.As to the initial size of a Mars exploration rocket, I think it makes sense to size the basic core to match the largest Earth orbit payload that is anticipated to have a reasonable flight rate (double the F9's 5 ton to GTO?), and build the Mars program around a 3-core version of that. Assuming the Falcon 9 loses 30-50% of its payload when it is made fully reusable, that suggests a Falcon X should have around 3x-4x the mass and thrust; so 25 tons to LEO for 1 core, 100 tons for 3 cores (Saturn V class).The colonization idea is nice for long term, but I think exploration with smaller rockets must come first (likely with government funding). So 3-4 Raptor engines, plus a center Merlin-derived engine for landing might be a better choice (the reusable upper stage could use a single Raptor plus 4 Super-Draco-derived landing engines); a smaller rocket would be built in a cheaper factory, etc.