Beats acquisition is bad because it means that Jony Ive is loosing his power.
Right after Jobs died the whole tech world announced that apple is doomed without him because Apple unlike other companies is very product oriented, vision oriented company. Tim has never been that guy, he's the logistics guy, the execution guy, efficient business guy. The spotlight turned to Jony Ive, detail obsessed designer, the closest thing to Steve we have left.
Here's the thing though: Beats headphones brake all the rules of what is Jonny's idea of good design. They are the type of product that somebody like Ive or Jobs would hate and despise with every cell in their bodies. Ive is know for being insanely obsessive when it comes to design and getting everything made just the way he wants it even if it meant reinventing the whole production lines or using crazy expensive technology just to get some tiny minor detail of the product right. I have a feeling that right this moment, Jony is pissed that he Apple will have something to do with substandard products like Beats headphones. It also means that Jony, probably the only "visionary" type in Apple that matters has been either overruled or had no saying in this acquisition. And that's pretty bad.
Buying Beats seems like a good business idea - the type of idea that makes shareholders happy - nice revenues, awesome margin, popular, trendy etc. Unfortunately, if you're reading between the lines, it may also be the sign of deeper issues that may harm Apple long term or even kill what made them so successful in the first place. I wouldn't be that surprised if Jony made an ultimatum "if you put apple logo on these headphones then I'm gonna leave". It sounds overly dramatic, but if Jony really believes in Apple, and what Steve Jobs stood for, then it doesnt seem that far fetched.
I'm also kind of surprised that Apple hasn't tried buying Bose - very similar design language, bose likes to put emphasis on their awesome technology and they have some good and establish products - their noise cancelling headphones are highly regarded and are de facto standard in aviation and their recent products like Soundlink Mini is everything that Apple loves: small, powerful, premium and aluminium ;)
tldr; Jony Ive would have never bought Beats because theyre not up to his standard, which means that he was overruled or has no executive power in apple. As the only "visionary" type in Apple - that means trouble.