[This is mainly to get my idea on record so someone might find it useful.]
I like the Smallville RPG, even though the source material makes me feel less than enthused about doing so (I hold that it is actually a game that transcended it's source material). So I've been mulling over alternative ideas for play, which is difficult, since it really is a nicely integrated game.
For example, the main attributes in the game aren't just characteristics, they are Values (Duty, Glory, Justice, Love, Power, and Truth) and the character can actually play against them by Challenging them.* So in the normal course of play they help you, but when you cross them they have a tendency to bite back.
So simply replacing them with a non-reactive characteristic doesn't seem right. Now with the latest incarnation of Glorantha a character's fundamental runic nature has a greatly increased importance. So it might well be possible to replace these six values with the five elemental runes (Darkness, Water, Earth, Fire, and Air). The nice touch is that elemental affinities run throughout Glorantha when you apply the condition runes. Taking Death for example, which often symbolises violence, you get the traditional various weapon combinations. So someone wielding a spear would use Fire; a sword, Air; a mace, Darkness; an axe, Earth; and a soft/entangling weapon, Water. You can carry out a a systemic replacement of skills with the other condition runes, such as movement (Fire = Ride; Air = Jump; Water = Swim; Darkness = Sneak; Earth = Endure [Hiking]). It also leads to innovative applications such as using Jump to "jump out of the way of the blow" instead of "dodge," and Endure to "block the blow with my shield."
One nice benefit of doing this is that skills now naturally become advantaged and disadvantaged against one another according to the cycle of elemental advantage. Thus Air always has an advantage against Water, but acts at a disadvantage against Earth, so someone with an axe would probably beat someone with a sword who will probably cut a soft-weapon weapon to bits.
That leaves the mammoth in the room with respect to 3rd Age Glorantha. What to do with the Moon rune of the Lunars? Now this is simple, since both Air and Moon are signs of the Middle Air [the realms between Earth and the Sky (Fire)] and each excludes the other. So Moon can easily replace Air (with Death leading to wielding a scimitar and Movement leading to Balance, etc).
But can we carry it further? What if we represent Chaos as a wildcard? And allow it to actually taint someone. What if we allow the player to substitute one of his elemental traits with Chaos. As a wildcard, it can be used in place of any of the elemental affinities because it is not part of Glorantha and therefore not bound by any of it's rules. But it's Chaos, so using it always has unintentional consequences. And people can hide their Chaos taint by simply not using it. Until they need it, at which point is waiting there for them.
Now I have to think of how one can Challenge your fundamental elemental nature, and what the results might be.
[And I still claim they swapped Clark Kent's Power and Truth Values – Truth should be a d4 since it is always getting him in trouble, whilst Power should be a d6 because it is unimportant to him (he is, after all, Superman, and until he loses his power it doesn't really matter to him. But since Superman stands for "Truth, Justice, and the American Way" they probably couldn't make Clark Kent the lying idiot he is in the show. And yes, the game convinced me to borrow the complete series and watch them. And it's a prime example of the failure of the American method of TV writing by committee – any character development in one episode never appeared in the next, leading them to appear even more petulant than the normal instance of teenagers.]