I've never been a fan of the 'three augments for one effect' sets. They just seem like way too much work for way too little benefit.
I get that they give additional value to all those items that don't have a set bonus, but think it through;
Assume you have terrible luck and never get the item(s) you are looking for to drop. Thus, you have to spend raid runes to buy them. After a great deal of effort you can buy three specific items that form a set, which will usually give you three 'set bonus' effects (sometimes more, rarely less... never that I know of at legendary levels). OR... you can grind twice as many raid runes to buy three items w/o set bonuses AND three items to convert into set augments to get ONE 'set bonus' effect. Twice the work for one-third the reward.
Using various 'non set' items from different sources you can potentially get that down to an equal amount of work, but the benefit is always going to be less... and you're giving up three augment slots for the privilege. You can do A LOT with three clear augment slots.
Maybe the 'gear tetris' works out that you absolutely need some specific group of effects and a three augment set is the only way to do it with the gear you have... but more often than not there is a way to do it quicker and with more benefits using items with built in set bonuses.
tl;dr
As such, I might suggest making it easier to create these augment sets. Let ANY item from the raid be used to create any of the augments... or at least have two or three options for each augment.
Also, you can't apply them to items that already have a set bonus... or double them up on one item. Therefore, they are taking item slots away from other potential sets. Since they only give you one effect, they should take up AT MOST two item slots, not three.