I'll say it again, the increase in this had absolutely nothing to do with pre-staging. If Gree didn't want players to be able to take that advantage, the solution would be simple. Just repeat missions several times like they did in a couple LTQ's already. It minimizes the benefits of pre-staging your missions. Or do 25 one-hit missions instead of 5, five-hit missions. There are options that make much more sense then "oh, just double the energy requirement".
This has everything to do with the fact that the LTQ's were completely unbalanced with the rest of the game. Selfishly, I'd love to see them like they were because you could get enormous stat increases for, relatively speaking, minimal expense. Couple this with the easy awarding of the +2 energy boost last event, and the problem was magnified even greater. Enormous stat gains from indestructible units for hardly any "cost". If it seems too good to be true... what? It probably is!
I've been wrong many times before, but I would expect that we'll see another adjustment to the LTQ's soon. They'll keep the mission count down from the earlier events, increase the energy requirements for each missions (as compared to early events), but keep the total energy requirement around for the event around 115-135k energy.
I doubt you'll ever see a 25k raw boost to your stats available for 2k gold again. We might be lucky to see 15-20 indestructibles awarded and around a 6-8k raw stat boost. But rest assured, the reason that is the case has absolutely nothing to do with pre-staging and everything to do with balancing the event.