What I've done to combat this issue is turn off bundling in the inbox. I already have filters for promotions and social to get archived immediately, so normally things that come in the inbox are only things that I need. And then about once every other day I go into All Mail and see if there's anything that I might have missed.

But generally I love Google Inbox, I use it with Mailplane on the Mac. The only problem is on iOS it doesn't show me a notification number on the icon for how many messages are in the inbox. Only the number of unread messages. Which, for me, I use my email as a general to do list, so if there's no number there I won't look at my email. Because of this, I use "Spark" on my iPhone and then Google Inbox on my Mac. It seems to be working well so far. I'm patiently waiting for Spark on the Mac.