I don't know if I've been unlucky twice, but I think the biggest problem I see with working at a startup is the lack of transparency on runway and the security of whatever form of compensation I am getting. Twice now (in 2 diff companies) I have been stuck in the position of finding out with only a few days' notice that paychecks are not getting wired and we're hunting an investor to bail us out.
Somehow it has become ingrained that a CEO's job is to build everyone up and paint the vision. Well, that's great but somewhere along the way we forgot about the basics of personnel management. Think a co-founder is taking a chance by going without a salary? How about the dude with options and a family.
Sure, people know what they are getting into when they join a startup - or should - but I yearn for YC's next class on "Startup Ethics 101".