There seem to be many experts who are diagnosing the problems with the ACA online system. I'm not going to join their ranks--I'm no expert. I expect only those on the inside, and only some of those, know really what has gone wrong and how hard or easy it will be to fix.
The one thing I will say (immediately contradicting the paragraph above) is that they shouldn't have changed the design to put establishing an account first, instead of putting it at the end. The problem seems likely to have been the change. It apparently was too late in the day to make it; they should have kept on with the general design they started with. That raises the question of whether they had buy-in on the system design from everyone, by which I mean Tavenner, Sebelius, OMB, and the President, well in advance.
The closest I've ever come to this sort of problem was the 1983 payment-in-kind program, in which the Reagan administration strongarmed the lawyers into a tricky device to swap CCC-owned grain for acreage reductions, a program which I remember as being slapped together in about 2 weeks (though memory is probably fallible). The Secretary had the Under Secretary ramrodding the implementation, because it was a high risk endeavor, and he had regular (daily?) meetings with the peons who were doing the scutwork.