Though it will probably be a while before we see a Hidden Ability Dragonite around, Multiscale seems woefully underpowered in ASB. Could we perhaps change it so it's in effect until the Pokemon drops below 75% health? Or 50% but make it .75 of the damage instead of .5?
I agree that Multiscale is pretty underwhelming; as it is now, an opponent can just game it by using a weak utility move like Thief or Nuzzle where the 2-3% blocked won't really be missed, and then the ability's worthless unless the Pokemon finds a way to heal back up to full (unlikely). I think that your suggested improvements are a little too over-the-top, though. If I'm doing my math right, the first one gives a Multiscale Pokemon an effective 125% health, and the second gives ~116%. My suggestion would be to change it to halving the final damage of the first move that would deal more than 10% (or 12%?) damage, so it would become a sort of reverse Sturdy. It's a bit of a stretch flavor-wise and doesn't fit that well with the actual game mechanics, though.
As for the abilities listed in the OP, I like the suggestion there about having changes affected by Contrary invert when they fade (though I think not all refs have the changes fade? Contrary could be a special case where, like, all changes invert in two rounds or something.) Then stat-lowering moves wouldn't be completely irrelevant - you could still Screech or Fake Tears a Contrary Pokemon if you're okay with waiting a few rounds for the boosts to turn into drops - and you can still "boost" up with Leaf Storm or Superpower if you're ready for those +6 boosts to turn into -6 drops after a few actions of being a super-tank (the damage you can deal in that time is limited by caps, too.) Other than that, I like Walker's suggestion on Telepathy and Superbird's on Protean.
While we're talking about abilities only effective in doubles, though: Flower Veil could be changed, but I don't have any ideas that don't make it
really good, since if it affected the Flabebe family too it would basically be a free Clear Body + status immunity. Friend Guard is mostly underwhelming even when it activates, since the utility attacks you would be directly targeting an ally with for whatever reason just don't do enough damage for a 25% damage reduction to be worth it in most cases, and spread moves already factor in the spread damage reduction. (Suggested changes:
all moves targeting allies do .8-.9x the damage? All moves targeting allies do .75x but the Friend Guard Pokemon takes the rest of the damage? Allies take no damage from this Pokemon's moves, like a reverse Telepathy?)
Also, uh... Plus and Minus are useless when you aren't in a double battle with another Plus or Minus, but when you are it's very powerful, so idk if that needs to be changed. I guess Regenerator, Unnerve, and Natural Cure also fall into this boat, the latter two less so, in that they're all really good in really rare situations - I guess Flower Veil would be in this camp too. I think Healer is just generally not very good right now, though; I would suggest making it affect the user only in singles, which would make it a quasi-Shed Skin: Healer can heal allies in doubles/triples, but can't heal the user in those battles, and can't do the two-actions-status-curing thing. I don't think Healer is distributed widely enough for this to be overpowered, either.
As for other abilities that aren't that usable: I find Intimidate to be a little underwhelming because it pretty much only activates at the beginning of battle and even then doesn't do anything half the time because the Intimidate Pokemon was already on the field when its opponent was sent out. I get this matches with game mechanics, but I don't think it makes flavor sense or balances well in ASB where sendouts are much less frequent, and its effect when it does activate isn't gamebreaking or anything. Rain Dish barely recovers enough health/energy to recoup the cost from using Rain Dance in the first place, and that's assuming the opponent doesn't change the weather in the middle; maybe it could be changed to 2% health/energy after each round, or just a flat 4-5% health? Magma Armor is kind of useless because freezing isn't very common in ASB and is much less powerful than in the games when it does happen, but all the Pokemon that get it have better options and idk if it would be worth changing/what it could be changed to. Also, Grass Pelt is useless because Skiddo and Gogoat don't even learn Grassy Terrain, but I guess that just means you shouldn't get a hidden ability Skiddo. The Speed boosts that Weak Armor grants are nice at first, but once you've reached a certain threshold getting faster doesn't help - maybe limit the number of times it can activate in a battle? Only Garbodor gets it as a normal ability, though, so I don't think it really needs to be changed.
(tl;dr: Multiscale, Friend Guard, Intimidate, Rain Dish, Magma Armor, and Grass Pelt, and Healer and Flower Veil to some extent, are all pretty bad right now, and some other abilities are good but only in specific, rare situations (so they probably don't need to be changed.) I'm not sure if I'm being overly change-happy here? I get that ASB tries to stick to the game as much as possible, but I think at least considering some of these changes would make them more balanced/worthwhile.)