To see if there was any patterns we might discern, here is a handy guide to the current spell list:
Banishment - Cha - Your force of will overcomes theirs
Blade Barrier - Dex - They avoid force blades
Burning Hands - Dex - They avoid fire
Charm Person - Wis - You twist their mind to like you
Cause Fear - Wis - You frighten them
Chain Lightning - Dex - They avoid magical lightning
Cloudkill - Con - They resist toxic gases
Color Spray - Wis - You disorient them (slow/weaken or confuse or frighten)
Command - Wis - You control them
Cone of Cold - Con - They resist cold
Destruction - Con - You kill them with death
Disintegrate - Dex - They avoid your death ray
Dominate - Cha - You control them
Earthquake - Con, Dex - They concentrate, they avoid falling over, falling rocks and/or falling into a hole
Finger of Death - Wis - You kill them with death
Fire Storm - Dex - They avoid fire
Fireball - Dex - They avoid fire
Flame Strike - Dex - They avoid fire
Flesh to Stone - Con - They avoid turning to stone
Harm - Con - You nearly kill them with death
Hold - Wis - You paralyse them
Holy Aura - Con - You blind them
Holy Word - Cha - You banish, blind, deafen, stun or kill them
Ice Storm - Dex - They avoid hail stones
Lightning Bolt - Dex - They avoid a lightning bolt
Meteor Swarm - Dex - They avoid fiery hail stones
Irresistable Dance - Wis - You make them dance, dance magic dance
Phantasmal Force - Wis - They see through your illusion
Planar Shift - Dex, Cha - They avoid being touched, your force of will overcomes theirs
Polymorph - Wis - They resist transformation
Prismatic Spray - Dex, Con, Wis - They avoid your disco lights, turning to stone or blindness
Sanctuary - Wis - You make them think twice about attacking
Sound Burst - Con - They resist thunder
Stinking Cloud - Con - They resist toxic gases
Suggestion - Wis - You control them
Sunbeam - Con - They resist your radiant beam
Sunburst - Con - They resist your radiant burst
Thunderwave - Dex - They avoid forceful thunder
Trap the Soul - Wis - You trap their soul
Wall of Fire - Dex - They avoid fire
Web - Dex - They avoid your webs
Zone of Truth - Cha - You make them tell no lies
There are some glaring inconsistencies. Sometimes you avoid beams/rays with a Dex save, other times it's just assumed to have hit and you make a different save (Destruction/Finger of Death). Damage/element type seem to have no bearing on the type of save made (sound burst vs. thunderwave). It's unclear what the separation of the mental abilities is (Int doesn't make an appearance, but Cha tends to be against outsiders, Wis against people). Almost all area effects are Dex saves, whether instantaneous or sustained (Fireball/Firestorm).
To me, when figuring out what saving throw a spell ought to use I would ask the following questions:
Does it affect the target's physical form, or their mind?
If you're unsure (Hold Person), do you think Wolverine or Professor X ought to be more resistant?
Physical:
Can you evade the effect through dodging the worst of, or all of it? Try Dexterity.
If there's no hope of dodging the effect, will it change/damage/destroy your physical form or make it difficult to perform certain actions? Try Constitution for the former, Strength for the latter.
Mental:
Would the effect only work on a concious target? Try Intelligence.
Does the effect involve the target's soul, or just their mind? Try Charisma for the former, Wisdom for the latter.
Hold Person, as an example, is unclear. You might say it's a physical force, and thus Strength, or a mental effect, and thus Wisdom.
Various elemental spells could do with tidying up. Either decide whether these things are Dex/Con based on the spell form (long-lasting area vs. instant or ray), or damage type (thunder seems more Con, fire more Dex and to me cold more Con and lightning (which doesn't act like real lightning at all) more Dex).
Illusions clearly require the target to be concious and should use Intelligence.
Charm probably doesn't affect the soul, whereas Dominate probably does, since it can make someone do horrible things. Perhaps define what your soul means, or what Charisma is vs. Wisdom, something is needed here.
Web is irritating, since it should just hit everyone and allow a strength save, but has a fiddly strength check if you fail your dex save.
Color/Prismatic spray should just assume you're hit and make you save appropriately.
