I have no idea magic was nerfed that badly. To me, it was physical attacks that were upgraded as we go along with the series. With the introduction of two additional rune slots in Suikoden II, we get plenty of rune combination to power up our physical fighters, while magic remained more or less the same.
Then, Suikoden III came along with its Skills system, and physical moves were further enhanced with the likes of Swing and Continual Attack, while magic suffered from the addition of chanting speed and concentration.
Suikoden IV somewhat took a step back in this direction, by stripping off a lot of those physical stats enhancement while retaining most of what magic had. In fact, the introduction of MP-replenishing items made it possible for magic users to be effective all the time, instead of having to conserve their MPs in dungeons for the sake of solely fighting the end boss. Having to fight without an accompanying guardian character was only a minor issue.
Rhapsodia. Magic were devastating, and if you are good, you don't even have to worry about running out of MPs. The Rune of Punishment was exceptional.