In my view we have (and have always had) two competing standards here:
1. Pulse Standard: Efficiency is the average number of pulses the uranium gives off per reactor tick.
2. Energy Standard: Efficiency is the average number of millions of EU given off by the uranium per reactor cycle.
Prior to the 1337 patch, which standard you used was purely semantic. They both yielded the same efficiencies in the same situations. Now that reactor output is doubled, standard #2 gives 2x the efficiency as standard #1.
Both are intuitive in their own way. We simply have to pick one to use.
Personally, I prefer the pulse standard, as it results in the same efficiencies as before the patch and involves the direct workings of how reactors operate.