After using Spell Mastery as written and seeing it more or less unused through RM2 and RMSS, I house-ruled it. Since spell casting is now a normal skill roll for me (with spell lists having a skill bonus with the same range as other skills), I just integrate the effect changes as a difficulty modifier to the skill roll, which basically means a lower change of success. This is more important for resisted spells or attack spells, obviously, since the casting roll is also the attack roll, but even then, it can get the caster into spell failure territory more often, which is basically the kind of balance I wanted.
In short : no separate skill, no separate roll, use modifiers.
And I basically agree with JDale here : spell mastery cannot duplicate the effects of such lists as spell enhancement.