The idea is energy champions are suppose to have the advantage in lane because they don't have to manage mana. As a tradeoff, however, they have no way to increase their pool of energy or how fast it regenerates, outside of using their kit in the "correct" way, which does restore energy. But apart from the mechanics within their kit, energy remains unaffected.
Blue buff is the one exception to this rule, because blue buff means the mid laners start to spam skills. The increased energy regeneration is probably there to allow the energy users to retain their edge in the lane, since without the extra regen, they would fall behind the opponents that they should really be out-regenerating.
Of course, this logic fails to include champions that use their health for spells, so those vlads and mordes don't really get any compensation for the costs on their skills. Unfortunate for those champions, but it does open up lots of other options.
I don't remember a mastery, rune, or item affecting energy, and I have been playing the game since season 2. That being said, my memory may be failing me or I just wasn't paying attention, but regardless, there are no such things now, and this is to highlight the fact that the advantage energy champions have early cannot continue to be exploited as the game goes on (CDR is less effective on them than on a mana champion).