I believe the Beetle is an improvement of the Boomerang, therefore it should be used in the Boomerang's place; however, I feel as if it was truly a one time thing. One could argue that the Boomerang is a staple to the series, but that's not necessarily concrete reasoning on why it shouldn't be replaced. The Beetle could preform functions that the Boomerang never could (i.e. picking up Bombs and dropping them on enemies). Even if that's so, we need to take into account that the Beetle is an ancient mechanism crafted by the Ancient Robots, and wouldn't necessarily be used in a more modern Zelda game.
I really prefer the Beetle over the Boomerang, but logically speaking, the latter is more likely to be used than the former. Also, no, I don't believe that the Beetle could potentially be a upgrade to the Boomerang.