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I think it is clear that the current concept of a set bonus is well past its use by date. The latest nerf to the shaman T9 4 set bonus is only the most recent example of why the current set bonus method needs to be changed. Some suggestions that are way more logical;

1 Fix the set bonus for all tiers for each xpac. Build all the "omfg I want to upgrade" stuff into the items themselves.

2 Remove the set bonus all together and just give each tier item an extra gem slot.

3 Make it so that an extra minor inscription slot opens for 2 set and a major one opens for the 4 set bonus.
Ghostcrawler
Set bonus more trouble than they are worth
I think gear might get really boring if you didn't have set bonuses (and perhaps trinkets) to look forward to.

Somewhat boring gear is okay... to a point... in PvP, where you need to strike a balance between skill and gear. Players want to enter PvP thinking they have a relatively level playing field, but we still use the gear reward as an incentive to participate.

PvE gear is already relatively inflexible on primary stats. If anything I wish there was more variability from tier to tier. Players have become pretty intolerant though of gear that doesn't feel like an unambiguous upgrade. That's not intended as an insult to anyone. It's just the state of a five year old game. :)