Clinton's biggest problem will not be the Republican candidate. Nobody in the shallow GOP bench has anything approaching her name recognition, experience, or political machine. Yet the troglodytes on the right will vote for whatever candidate manages to fill that position.
As such, her challenge will be voter turnout. She needs to get independent voters and those Democrats who think a Clinton win is a foregone conclusion to nevertheless drag themselves down to the local VFW hall or school gymnasium and punch a few more chads than the Republicans.
I don't think name recognition will be a big problem for the Republican nominee. It gives her a big edge in the Democratic primaries, but I don't see it being a big problem for the general election. Was Obama better known than McCain going into the 2008 elections? I don't think so.
As for experience, she has one term in the Senate and a very controversial stint as Secretary of State. Not exactly an awesome resume. And as for machine, the GOP has every bit as good a political machine as the Democrats which I think you acknowledge indirectly by pointing out that her big problem will be turn-out. And yet, in 2012 it was turn-out that hurt the Republicans. Lots of born-against just weren't in to voting for a Mormon. I don't think 2016 is going to be a slam-dunk for Hillary or any other Democrat, but at this point, the likely GOP nominee is very much up in the air moreso than at any time that I can remember. Republicans don't have a habit of nominating dark horses and yet at this point, everyone seems like a dark horse.