I'm doing the same strategy for rebalancing that QQQ does, and I figure that the headache of tax time is a "Tom in 11 months from now"'s problem :)
Some tax software nowadays will allow you to simply upload the tax documents with all the transactions and it will tabulate everything for you, so I don't think it will be too hard for me.
I'll admit that there's primarily just kind of a coolness factor to be able to say that I ripped off and copied QQQ without any fees, but I do genuinely like the idea that I can avoid companies that I think are terrible in the process.