This is working as intended. Bungie didn't want people just playing 3 characters of the same class to speed up level and gear progression. Not only do you not get the well rested buff but powerful engrams from the milestones are nerfed for the other two characters. In other words there is no benefit to playing with three identical characters, None. Roll one of each classes and you won't have to worry about it.
Just curious but why 3 of the same class, what's your reasoning for doing it?
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I just like the play style of the Hunter better than the other two class. And when I did have multiple classes it took me too long to get used to the double jump. Plus have 3 hunters allows me to collect all the armor without completely filling up the vault. And I do understand the milestone and powerful gear nerf for having 3 of the same class, and am perfectly okay with it. My only concern is that well-rested only effects bright engrams, which only rewards cosmetic items, that have no effect on power level.
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So for having multiple classes taking to long to get used to double jump. That's not a problem if you don't play the other two classes and only play your hunter. As for the vault space same thing. You don't have to play them if you don't want to you'll still get the vault space boost. If you really don't like the other two classes but want the bright engrams then just play them for 30 minutes and get the 6 bright engrams and then go back to your hunter. They don't take long to get with the well rested buff. You will have to get them to level 20 though first.
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Not trying to argue or anything, because I do see the point you are trying to make. But, if I have the 3 classes, I would not be able to collect the armor for the Hunter from the 3 factions. And that would really annoy the collector in me.
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You can pledge a different faction each faction rally. So while you won't be able to get all 3 the first time around you are still able to get all of them eventually.
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That is true assuming they don't change the faction gear every season. But if they do, I would be SOL if they only have 2 faction rallies every season. But they could bump it up to 3 since Bungie was slowly releasing the endgame during this season. But I would rather be safe than sorry.