The thing about badges is, it's a collection system. It was created for people who enjoy a collection mindset and playstyle. And players who enjoy that will never be okay with having 99%. The entire *purpose* of a collection mini-game is that the player is working toward having 100% someday. They go into it knowing full well that the last few items will take patience and persistence; it's what they like about it. They enjoy pushing themselves to "cross the finish line", so to speak. Except when unique and time-limited items are thrown into the mix, they'll never cross that finish line, and they know it. Because there will be items they literally can *never* obtain. For most collectors the only thing that's going to do is foster negativity.
I say, if you want to have rewards that are time-limited or unique, just leave them out of the collection mini-game. For example, CoH lumped everything into badges under various categories - Achievements, Accomplishments, Events, and so on. If there had just been a section for these things where they weren't included in (or left out of) the character's badge count, I think there would have been a lot less resentment from the folks who didn't have them. The badges themselves would have been for things the *character* did (and those would all be things that could be done again at any time by any character, regardless of creation date), while a separate system would track what the *player* had done (things like log in on certain dates, attend events, or win contests).
I think that would be a much better way of handling things, without having to completely do away with unique and time-limited rewards. Because I mean hey, those are still cool for the people who can actually get them. I believe they're only received negatively when you put them on a checklist while knowing that the majority of people will never be able to check them off.