Wikidata is the way to go. If you manage to get a machine readable form of Wikipedia knowledge which is not yet present in Wikidata, please consider contributing to Wikidata.
Good point on this too. I think there's value in allowing and exploring one-off / alternative views into Wikipedia especially where the data isn't accessible already - but long term any serious effort should be merged back into (or at least offered) to the official source.
I actually hope the WikipediaQL, when it will become a bit more mature, to be helpful in parsing Wikipedia data _into_ Wikidata. As of now, Wikidata lacks a lot of knowledge yet (the article talks about that, too).