I've owned both over the years and I'd say TOM is the better game overall. TOTAN has some REALLY annoying sound effects and worse rules. The pop bumper area may be the worst designed in any game ever on that game. TOTAN is easier to "beat" also, especially with the rubies wishing away modes. Both have some cool magnet effects. TOM shoots a little smoother and has better modes and shots. Both have cool outlane saves.
If I had to own one again it would easily be TOM.