On taking office Mayor Hales took control of all city bureaus. In effect Portland has not had a commission form of government in that time, it's had a strong mayor system.
The problems with implementing the arts tax can't be put on the commission form of government, they belong solely to Hales. By changing deadlines, monkeying with the definition of who was subject to the tax and generally badmouthing it he's given Portlanders every indication they should ignore the tax. That so many have paid anyway is a testament to how popular the idea of putting art teachers in schools is.
The "kinks" in the arts tax demonstrate the weakness of a strong mayor system, wherein a city's priorities can be totally re-written by the election of a single office. It encourages short term thinking and a focus on what one person can do in a four year term, rather than thinking about what a city should do in the long term. And it's impossible to adequately vet candidates. The arts tax drew more votes than did Charlie Hales, is it likely that people supported him knowing he'd undermine the tax?
Portland's problem isn't with the commission form of government, the problem is that we've abandoned it.