The main problem with Yakupov's NHL career was that he simply wasn't an exceptional hockey player. I really don't know what the Oilers (in that awful Steve Tambellini period) were thinking. Sure, he was likely to go in the first round to somebody, but as a 1st overall choice, he was an odd one. I remember watching him play -- it was, like, his third NHL game or something -- and my opinion after one game was, "This guy sucks". And nothing I saw over the next few seasons altered my opinion. (And he actually had a statistically decent rookie year, but I thought he was a whole lot of nothing.) Yakupov was a good skater, but so what? So are 90% of NHL-ers. He had terrible hands and could not process hockey at NHL speed.
A secondary issue with Yakupov -- as Brian Burke crowed (as usual) in pointing out -- is that he had a bit of weird attitude and psychological make-up. This (understandably) scared away some other NHL franchises from drafting him. Giving interviews where he said there was "nothing" he needed to improve didn't exactly endear him to fans / media / teammates.
Finally, a third, if lesser, factor in Yakupov's poor NHL transition was the Oilers firing coach Ralph Krueger after Yakupov's short rookie season. Not that Yakupov did anything amazing as a rookie, but he scored enough and had a big enough role that his confidence wasn't shot yet. But just four months into his NHL career the Oilers hired a new GM (MacT) who fired the coach (by Skype) and hired... Dallas Eakins. With very young players who are struggling, sometimes changes coaches in mid-stream can be a disaster, and it was with Yakupov.
Of my three points, though, that third one is relatively unimportant. Yakupov could have been drafed by any NHL franchise and he would have struggled to succeed.