The bulk of the article is concerned with how HR3200 is an unmanageable mess because it's really really long and makes reference to lots of other laws. Well, surprisingly enough, this is how just about every other piece of legislation ever looks. Laws are not written in, and do not exist in, a vacuum. There is a tremendous body of legislation that already exists. New legislation has to modify parts of that existing legislation, while keeping other parts, deleting still other parts, and ignoring completely other parts that aren't relevant to the new law. It's sort of like revision control in software, except instead of having a bunch of diff files in the background and having the new law be the final combined output, the new law is basically a diff file itself, which in turn modifies earlier diff files, which may themselves modify earlier diff files, and so on. The entire revision history is kept in the legislation itself, basically.
And that itself is a problem. Ever try to actually read a piece of "important" legislation? I have. Once. I gave up. It, like this one, referenced not just numerous other laws, but different books of law, like US Code, IRS Code and such. And to understand the effect of the ones that change those, I had to read large sections of other laws. And you know what? Those sections referenced other sections, other laws, and multiple struck out laws which I then had to look up their replacement to see if that was still in effect. If you pick a particularly bad line of a bill, it could take reading 1000 pages of other laws to understand that one line of a 1000 page piece of legislation. For one, that can lead to unintended consequences. For another, I would expect that no legislator actually reads the bills from start to finish with complete understanding, but instead aides read parts and summarize. Not that it's a particular problem, but if ignorance of the law is no excuse, how can people held to the law be expected to know it if the people that pass it don't even understand it?
HR3200 is very long and complex because it's seeking to overhaul a very large and very complex system with a vast number of laws already written about it. HR3200 has to modify a number of these existing laws in order to do what it aims to do. Frankly, I'd be worried if it came in at much LESS than 1000 pages, given the scope of what it is trying to do and the vast amount of legislation that's already been written regarding health care.
Rather the build on previous laws, with great modifications, it makes for better readability and no reduced functionality to just repeal laws with large modifications and integrate them into the new law. Or, better yet, do it like software. Group three or four laws together. Have one on funding, one on coverage, or other separations that group functions into easier to read and understand segments that are self contained.