I like the idea of the Beetle for sure, it's much more convenient and it adds a sense of challenge when retrieving such objects/hitting buttons etc. not to mention it's rather fun. However, the boomerang is such an iconic item in the series, maybe not to the extent of others but it's appeared in most Zelda games and to be honest not seeing it again would feel quite strange.
However, I can see this manual control returning in some sort of format, think about the Gale Boomerang, this was definitely an interesting twist and I'm sure this could be manually controlled much like the Beetle. Though I do feel the Beetle just seems like the better choice since it worked quite well in Skyward Sword.
Would this leave the Boomerang useless though? Hmm I'd have to argue with that, the Boomerang is much more of a quick way of grabbing items as well as stunning and fending off certain enemies. If it's one thing that the Beetle lacks it would be its efficiency and it's use in combat. Maybe the Boomerang could be an alternative way of retrieving items in plain sight, the Beetle would go for a more advanced route, although the Boomerang could be made much more prolific in combat. I look at a game like Ty the Tasmanian Tiger , which used Boomerangs as it's main form of combat, and there's potential there - maybe building off the concept of mixing in elements with items, much like the Gale Boomerang.