I'm not worried yet. It's still early days. If he still hasn't featured much by December, then I'd start asking questions. As it stands, it's understandable that he's behind Rooney/Mata, which makes crashing out of the COC even more frustrating. We're facing difficult opposition in the next month so it'll also be unlikely that he'll feature much then as I'm sure LVG wants a settled, strongest 11.19 year old players don't develop by sitting on the substitutes bench. That excuse is paltry. Rooney, Ronaldo, Fabregas and Messi weren't sat on the bench at that age, and neither were many other players now currently near the summit of the game. Januzaj should be playing fairly regularly and if and when we finish top four this season, Van Gaal should be doing all he can to build the team around him going forward. We have an exceptional talent at the club and we should never be left to wonder what if. I'm not worried yet, though, I just don't agree that rest is best.
He did look burned out near the end of last season so it's understandable that the club wants to make sure that they don't Sterling him. I'm sure Giggs of all people would know how to manage Januzaj given the similarities between the two of them at that stage in their careers.