Like I said, earlier, I generally find the "Everything Crafted is Better?" style to be worse than the other ways. It makes loot less interesting, and makes you want/need to do crafting on every character. Yes, the ideal is that all the different combos are equivalent, so that you can among various options depending on your preference. The reality is that, just like with normal loot items, some things are better than others.
But not everyone picks their stuff solely on "gotta use the best". Some people will want to go with a theme ("my guy is really into laser shotguns! "), or a look, or whatever. If the crafting system helps with this? That's great.
Not everything in a crafting system has to be something you'd want to use, for the system to be good/valid.
(re: Skyrim. Personally, I never really super-uber-charged anything. I used Smithing to make & improve stuff, sure. But I didn't insta-max it to 100, stack multiple bonus enchantments & potions, etc. My first character with maxed-out Smithing - first skill to 100, at level 46! - was running around with weapons that did ~110 damage.)
edit: it was also pretty disappointing in Kingdoms Of Amalur - I had really high Smithing on my first char in that game, and never ended up using any of the named / rare / unique / etc, gear that I found, because the stuff that popped out of crafting was just leagues better. Next character I made, I only took a bit of smithing skill, so that I could repair my gear reasonably.