It never crossed your mind that you can use the silent running (with it's incredibly slow drain rate) when you need it and turn it off before it takes down a bar?
I never had an issue with not having enough energy, but I was always careful with turning abilities off before they consumed an entire bar, unless I needed to. In tandem with x2 takedowns and the stun gun, you're doing something wrong if it's a problem.
Why didn't you think of this?
PS, Stealth doesn't use an energy bar either, it drains over time, don't be a spazz and time things.
Many times I've used cloaking and silent running together to dart from one box to another without using a single bar up, helps to have faster sprinting too.