I'd say that our financial position (whether we like it or not, as fans) alone makes it unreasonable to claim we're the worst run “elite” club in Europe. We're a club that has kept sticking to the classic British managerial model – which involves an inherent risk: If the bloke isn't up to scratch, the club will (obviously) struggle results wise. Plus, it's an expensive model – if you intend to keep challenging, that is. You have to hire new managers, at great cost, who will need new players, at an even greater cost, etc. The continuity a different, more continental structure can potentially ensure, isn't there – obviously.
But we have the money. And the owners are clearly willing to splash it. I can't say I like this approach (keep hiring, keep buying, until it clicks), but if Mourinho now gets it right, I don't think one can claim that it absolutely doesn't work. A few seasons in relative turmoil after Fergie's retirement (but with ever more cash flowing in, in spite of poor results), then back to challenging properly – it's hardly shockingly bad.
While I don't think that the club is terribly run because of what you mentioned. We clearly have a problem with the sporting aspect of the club who seemed amateurish until the appointment of Butt who seems to be full of ideas and fairly decisive.
As for Mourinho, the club just hired the most reputable manager available on the market, you can't really criticize them for that but at the same time you can ask yourself what they would do if he wasn't available, they don't seem to have a clear profile for the United manager job.