I used to agree that Novas should be limited, and it even matches fluff, but my secret passion has always been to match another part of fluff: the part that says novas have always been lesser used than torps because torps are more tactically reliable and fit the fleet tactics. Hard to do in game though, when the alternate of the torp volley can cripple a cruiser in one hit and reach anywhere on the board.
But I can still dream.
One idea, in the vastness of space, would be to simply be roll a d6, miss 1-2, one hit 2-5, direct hit 6, or some such.
Scatter and blasts hitting multiple ships be damned.
Another limiter would be RO to reload the huge thing, never understood why it wasn't RO in the first place.