IMO Crafted gear, at least in a single player RPG, should always be better then found gear. MMO's this should also hold true, but there should be "Raid Drops" that are needed to craft items that are better then the gear found in the raid.
Here is my logic:
1. Found gear will be obtained no matter what you do. You are going to kill that dragon eventually, so it means every character is going to have the "Sword of I Pwned a Dragon". Its not "Special" and you didn't have to do anything to get it that every single other player who is playing the game didn't or isn't going to do eventually. IE. it 100% guaranteed loot that everyone will have, and as such should be designed in such a way to be "good enough" to beat the game with.
2. Crafted gear, on the other hand, requires a player to invest skill points, time, effort, thought, etc into making items that a player who chooses not to do these things wont have access to. A player is choosing to use your crafting system, it is an optional component, not something that is a 100% guarantee that a player will do it. As such, players who choose to invest in crafting should be rewarded with "better" items earlier then if they would have just spent the time killing the Dragon.
If both are "Equal" then there is never a reason to bother with crafting. If you can do and experience everything in the game without ever once crafting anything, then the crafting system is a waste of time.
IMO, DOS:EE falls in the realm of, not enough "power" in the crafting department to really make it worth putting more then a single point into it (from a min/max perspective, maybe you like crafting). The same is true for lock picking, as 95% of doors in the game can be opened with a key.. and usually the key is only meters away from the locked door... such a wasted skill... but I'm digressing now.
I personally would like to see the crafting system revamped in a mod to make it more complete for one, but also more useful overall.