So far I really like the new system. IMO you could take it further - I'd invest in ally missions that took a week or even a month complete if it raised chances I could get a rare and useful (and pink!) drop.

Beyond that - I do wish for in game help for game mechanics. Tell me how lesser/minor/major/greater mystery drops compare, how rare items are (% drop rate at least), stuff like that.

Summary - I'm pretty happy so far and give you my thanks for a good update (even though I was happy with the previous energy system too.)