It's condensator's (and reflectors have charges, technically - or use iridium. I have no idea if the iridium plates have charges or not as I've never used them but I hope not), the only way you can get significantly more EU out of a plutonium reactor (note: not efficiency, late game I hardly consider efficiency important and early game I doubt you are running many reactors to even bother with plutonium compared to uranium) is by using condensators. Condensators are pieces that are a void for heat, the heat goes in and disappears. They can absorb 100k's of the stuff, millions in fact I think. The problem is that they need recharging, with lapis/redstone. This means you need to have many more cells and a CCraft/redstone timer rotation (or some other form) to really exploit their usefulness, or you might as well have an on-off switch reactor that only runs while you're online anyway.
Most people don't use condensators. I don't bother right now. I might when redstone is in the pack and you can easily use timers to sort out the whole refreshing of them. Until then it's too much hassle.
If someone can make a plutonium MK-1 reactor with no parts that have to be replaced with over 400k, it'd be a start. Even then you're only just beating uranium which is 16x more abundant, and probably cheaper to run as well.
Also, MK1 is really the way to go at the moment. The old IC reactors with simple water and ice and what-not rewarded you for higher MK's, I honestly don't believe that the current reactors do. You'd be better off building 10 MK1 reactors than 1 MK5 that gives similar output even if you can control it in most cases... the only limitation these days is copper. If you use mystcraft dense ores (if this still gives copper), or twilight forest hill mining, or just generally a load of quarries, copper will be easy enough to get.