I would argue that the most glaring problems with the Affordable Care Act came from the overly lengthy process that it went through. By the time Obama announced his push for healthcare reform to a joint session of congress in Feb, 2009 most of the issues were already well-understood and it was just a matter of choosing from existing proposals. By July, the House had already passed several competing options through committee. The Senate held hearings for months hashing out various provisions. The House passed their final version in November and final passage in the Senate was Dec 24th.
From starting gun to final passage was nearly a year. That was enough chewing over for every possible special interest to take a bite. This, to address a problem that Teddy Roosevelt recognized, using a conceptual framework (universal insurance) proposed in the Nixon administration and using the precise mechanism from Romneycare that had been working since 2007.
Between intense, ongoing special interest lobbying, and the pushing and pulling to try and gain individual votes, the hashwork left in November wasn't at all pretty. In addition to the looming change in Senate control with Scott Brown's election, December meant the end of the 111th Congress so after an exhausting year of work Congress would have had to start all over. So, they took what they had and went with it. A much cleaner version of the same bill could've passed in July and would probably not have given the impression of passing a hastily put together piece of crap.