.hack//Roots

this also takes place in a vr would where players seach for mysteries. Do these mysteries really exist? 

both characters of the anime are conscious inside the game and in Sword Art online when the character is defeat he/she also dies in the real world while in .hack//Roots when the player is defeated by Tri-Edge they enter into a state of coma.  

It's similar 'cause they're both based on the sucked in the game-type and if you lose you die. (Except in .hack you go into acoma) Both also have the same protagonist, male. They both show adrenaline-pumping scenes, preferably Sword Art Online. 

Both series take place in an MMO world which evolves into a darker theme than just having fun and playing the game. 

These anime's are similar in regards to both of them taking place in online video games. I was a fan of the .Hack games and yet found sword art to be more exciting. The animation is more fluent, and the fights are definitely more intense. There's a more threatening atmosphere then in .Hack, since in .Hack you go into a coma if defeated by Tri Edge where as in Sword Art Online you die if you defeated by anything. The show becomes a little obnoxious after episode 15 or so, but I'm not an elf fairy kind of guy so you might think differently. ^_^ 

Both anime involve a male MC inside an online game, both MCs make friends inside the game and they are fighting together.What goes on in the game is affecting the outside world.Both games are run by shady companies in the real world.