You have not missed much by not playing past the GBA. The DS games were a sharp decline in quality over the GBA games, in almost every way. Even some of the gimmicks felt forced and there solely to have a gimmick.
as for SoTN, it cannot be blamed for what happened after. So No, I'd say that SoTN should stay. in a theoretical time travel retcon though, I would have advised against moving to the GBA.
They should have stayed with the PS1 for a while longer, then jumped to the PS2.
I would point at Mega Man, which I often compare. It stuck to the 2D PS1 style for 2 more games past their PS1 debut, and then jumped to the PS2, where results got fudgy in a similar way to when CV first tried to do 3D. (difference being it wasn't REALLY Capcom's first 3D Mega Man game, though it WAS the first 3D attempt at the classic formula)
I think that had they stuck to the PS1, the production values would have been higher, and there might not have been nearly as much asset reuse.
I guess in general I'd just keep SoTN, but advise IGA AGAINST trying to make SoTN 2.0 and making lightning strike twice. Because in doing so, the franchise stagnated terribly.