The system we have now, you have the flexbility to hold a charge for burst windows or use w/e you wants. With this ''cd overflow'' the game is pressuring you to use the action and not give you that flexbility, in some fights that have a long downtime, this is a very bad idea.

People store charges for burst windows because this is the most optimal way to have the most DPS in a fight, you don't need to do this, because only a small part of the content in the game have DPS checks like Savages and Ultimates.

Theres no flaw in this specific system you are pointing, 2 minutes meta is the real problem here but again, 2 minutes meta only matters for a small part of the game content that are Savages/Ultimates.