The one downside to the resource mechanic is that it feels penalizing to have more than one battery. This devalues all battery upgrades except faster regen, as a result.
I know I'm not the only one, but I've not had more than a single battery charged since the first enemy in the first mission. Takedowns become too expensive when they get rid of a limited resource. Same for punch-through-walls. And then once that resource becomes unlimited, you're not really wanting to go back.
I might eat an energy bar later if I really really need to use cloak for more than 4 seconds. But that's the only reason I can see for it. I'm thinking that all bars need to recharge, even if depleted. Just slowly. That way there's some actual value there for more regular use.