I think they're both worth it even if I rarely use them. Having them leveled and available as an option gives me a lot of inner peace :P.
You need the JC to craft the higher level gems (past flawless square) cheaper. BS crafting is inferior to AH shopping for the most part though.
And it doesn't cost THAT much to level them. It's a one time thing you have to do within all the years? you'll be playing the game. Their levels don't disappear when you die. So... why not?