Ghostcrawler shows up in the thread and says that the game would be pretty boring if set bonuses weren't included -- I presume he means that you'd just upgrade your gear according to iLvl, and that would be that. He even says that he wishes the tiers varied more, but players really want to see "unambiguous upgrades" to their items. People need rewarding when they move up, so GC can't mix things up with the various bonuses as much as he might like.
Obviously, I don't agree the set bonuses should be done away with -- I think they do add a nice twist to the game in terms of making interesting choices with your gear. And they also provide direction in terms of upgrading (in fact, I wish there were multiple lateral sets to choose from, much like we had back in the late vanilla game -- do I want this set bonus or this one?).
But I also think the problem could be solved by expanding choices in terms of gear. A while back, the set bonuses were changed from a full nine piece set down to the current five pieces, so that people would have more flexibility in terms of choosing their outfits (rather than locking everyone into a full set all of the time). And I think that was a good idea, but I don't like that we lost the full set. I think Blizzard should keep just the two and four piece set bonuses, but then expand them out into nine pieces of gear. Include the boots and bracers and belts, but leave the bonuses at two and four pieces. That would give us more options in terms of building up our characters, while still leaving us free to collect the set pieces as we wanted.
Of course, there's a lot of other balance issues there (you'd be able to set up two set bonuses, and who knows if Blizzard ever planned for that when they designed gear). But I think rather than removing set bonuses, Blizzard should let us do a little more mix-and-matching.