When I played Soul Hackers, I played basically every part of the game besides bosses with just Nemissa and Protagonist. I was rolling in Mag most of the game.
Not long after the Amami float, you turn a corner where MAG will no longer be an issue for you. Before that, using an encounter increasing item or spell every now and then will net you more than enough to keep going.
SMT I and II have a better overall feel. The beautiful graphics and cyber punk feel is cool in soul hackers but SMT 1 and 2 and have something Soul Hackers Doesn't that I can't quite explain.
On the 3ds version, you can swap down to easy mode on the fly and gets loads more MAG from battles and collect the stuff really easily. Particularly if you got walking around the hotel, there must me something special about that red carpet as it generates so much MAG.