It's easy to tie crafting into endgame gear. Drops from raid bosses can't be dropped, and they can only be created by crafters who have killed the boss (character flag) and the gear can only be worn by characters who have killed the boss (same character flag!).
Voila; best gear in the game as an average is crafted but can only be used by people that have actually beaten the content. Think POT from EQ, except instead of the dropped turn-in stuff being the best, the elemental crafted stuff was the best and only people with the proper elemental filled stones could equip them. Same shit, more modability/choice on what gets made, and you end up with less rotting paladin crap.
Yeah, there are plenty of ways to design this well. Problem is there are more ways to design it poorly. Just like every aspect of an MMO.
There's also the question of how much "better" a crafted item is or if it's augmenting raid drops. So perhaps you take your Hopebringer from PoTime and it has an augment slot (type 8). Maybe the best type 8 augments are crafted from raid dropped materials, or a separate raid-only drop can be applied by crafters as an additional augmentation (perhaps with options – would you like +1 damage, +4 AC, or +25 HP?).
FFXIV has an "overmeld" system. Most armor (and weapon) pieces have two materia slots (and accessories have just one). If that armor is crafted (instead of vendor-bought/dropped), then crafters can apply up to five materia to the armor, but the chance is reduced and so it can be quit costly (a typical materia "meld" is always successful, but the 4th slot has just a 7% chance of success, and 5th slot is only 5%). This combats inflation while providing marginal gains for high prices.
Perhaps that crappy Paladin sword doesn't drop at all – instead of the Hopebringer, you get shiny_sword_hilt_73 that is a component used in the creation a weapon for any tank class. This shiny_sword_hilt_73 is no drop and used by a crafter to create shiny_unfinished_sword_73 which is droppable but must be combined when equipped with shiny_smithy_gauntlets_73 that are no drop, come from another PoTime boss, and consumed upon use. This would require you to have crafters on your raid team, creates a money sink for end-game players, results in less rot loot, and doesn't filter down the best drops in the game to anyone who doesn't "deserve" it.
Or maybe the most epic sword in all the land, Excalibur, requires you to do tradeskills as a hurdle in the quest. Maybe crafters can sharpen that Hopebringer from PoTime and create a Hopebringer +1.