I think part of the SoTN magic is that it was hot off the tails of Rondo- it is, a sequel to rondo, so the visuals were still really fresh. It reused some of Rondo's assets, but considering it was a direct sequel, and it was the first game to do so, it's not noticed. it also added a lot of original assets.
Later games however, just fell too into the habit of reusing rondo's sprites, so that we were seeing the same goddamn skeleton years after he originally appeared. So the visuals got a little stale in some areas.
Another issue, is that despite trying to recapture that magic, IGA didn't seem to realize, that the gameplay was good. Instead, he tried to push many different gimmicks, because thats how he designs. gimmick first, game and story after. Some gimmicks worked better than others, (the Soul system was basically just a fancy subweapon and ability equip system) but yeah. That's my 2 Cents