Two points here.
First of all, the story of the 2 month player that is now 90/90/90 crafting is leaving something out. The amount of grind he spent to get there. If he'd spent as much time adventuring as he's spent in the crafting hall he'd already have multiple greensteel items, dual greensteel weapons, and a slew of raid loot. With the crafting grind what it is I'd assume he could have easily capped a character in about 2 weeks w/ the same level of dedication and outside help (probably faster).
Just for the sake of argument let's go with 2 months and 2 weeks in game. After capping that's 60 days of pure raiding/epics at level 20. Let's say he runs nothing but raids and some key epics for those 60 days at cap. He'll most likely have at least one of the key items he wants from each raid at that point. He'll most likely have at least one epic item that he wanted to focus on slotted. Again, we'll probably see a greensteel sp item and a greensteel hp item as well as a greensteel weapon or two (assuming he did some good trading to get there or had some help from friends).
Instead, he's level 16 and he's able to make an item equivalent to the greensteel weapon he'd have anyways. He can do that over and over. But he's still going to be lacking a ton of raid/epic items. It's a tradeoff. He chose the crafting path. The time he put in is roughly equivalent to what it would take to devote enough time to capping in 2 weeks and then running all pertinent raids/epics on timer for 2 months. I think the return, when put in those terms, is fair.
Now the second issue. As I've mentioned elsewhere, the crafting shards don't need to be made harder. The shards of potential do. What does anyone care if I make a +1 longsword of greater lawful outsider bane? Is that breaking the game? Not even remotely. It's the +5 silver holy burst khopeshes of greater lawful outsider bane that need to be closely controlled. You can control those by making the high level shards of potential either timered or prohibitively expensive (without raid or bound named loot).