The check-down on 3rd & long will be a fan favorite in no time.
Better than over throwing a go route to a covered WR on 3rd and 6th
It's really not though. Low risk, high reward is always better than low risk, low reward.
It's all situational. If you have a QB who excels at throwing go routes and have a receiver who is solid at winning jump balls then maybe a decent idea on third and long. However I would rather have a QB who doesn't force a bad throw and gives a good playmaker a chance to make a play. You don't want to have check down Sam Keller out there but an appropriate and properly executed check down is a very good option.
Obviously neither thing we mentioned is optimal, but throwing deep on 3rd & 6 is better than checking down on 3rd and long. Generally speaking, the best case scenario on the deep pass is a big gain. Worst case scenario is an interception, which is effectively a punt. On the check down on 3rd and long you're punting either way. But at least your completion percentage looks better at the end of the game.