For simplicity's sake, I'm going to give you the answer provided by Skarn in yesterday's comments:
If you want follower gear, open them now. In 6.1, crates will no longer give the "upgrade to 615/630/645" pieces. They will only give the "add 3/6/9 levels" pieces.
For player gear, I think the change is neutral. So open them now!
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Will there be some new quests (normal or dailys) to get rep with WoD factions, for players who don't like to grind mob for rep ?
As far as I'm aware, no. You can either grind mobs for them or ... grind mobs for them when you get the right Apexis Daily.
That's about it.
any chance at a garrison app to control missions and work orders?
Unfortunately, no. I'd love to see it, but Blizzard has said there are no plans for it. Garrisons may or may not carry over into future expansions, and if they do, they won't take the same form they do now. They would be creating a mobile app as a companion for only one expansion and then it would be dead and useless in the next.
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