That multiple-opponent-per-takedown aug sounds cool but really, how often can you sneak up on two guys?
In my experience: quite often. In fact, that was one of the first augmentation I've picked on my second play through.
We were wondering about the energy cells first as well (I'm playing this game also on the PS3 together with a friend). But I guess the game would become far too easy if the energy cells would all completely recharge automatically. So far, I have only upgraded to faster recharging, which in my opinion is already enough for most parts of the game- if you don't use energy-hungry augmentations such as invisibility. There's however one particular part where quickly taking down all enemies is crucial and the additional energy cells really become helpful.
On my first play through I was still carrying lethal guns with me for taking out the bosses. But now, on my second play through on PC (aiming for the Pacifist trophy), I don't care for them anymore. Bosses I take out with grenades and mines and the only gun I take with me is the tranquilizer gun, which comes in handy in a few situations. For most of the time I simply knock enemies out though.
I'm planning to upgrade the Typhoon though for taking down at least one of the bosses. Don't know if it's worth it but I really like the animation.