I'll compare them simply on which one I like better overall...
MS3 is better.
Why?
Well, it's a 2D masterpiece made with such a loving attention to detail that it makes your eyes hurt. This game is also the current high-water mark for 2D side scrollers.
Radiant Silvergun IS really good, but there are other Saturn shooters that I think are even better. RS is good because of the innovative gameplay and somewhat revolutionary overall presentation.
I make this judgement based on this tried and true question: "If you had both and had to give one up, which one would it be?"