Ditch traditional statistics
Not only do the current statistics obfuscate actual gameplay effects, they feel outdated and cumbersome. Strength is a primary offender - it's needed for inventory space and item equip requirements, even though 1) the former really has nothing to do with strength, except in a traditional sense, and 2) the latter is subverted by stacking +str equipment and abandoned in the face of strength-scaling skills. Removing these statistics would be an incredible endeavor - you'd need to change many stat-dependent calculations, stat requirement for items and talents, and completely reevaluate NPC's stat distributions. Crazy, right?
Replace old stats with more open, directed choices
(Ignore the names for now, I'm having trouble choosing something that sounds right. The numbers, where shown, are meant to exhibit the relative bonus.)
Physical
- +Physical Power(3)
- +Physical Save(3)
- +Physical Crit
- +Spell Power(3)
- +Spell Save(3)
- +Spell Crit
- +Mental Power(3)
- +Mental Save(3)
- +Mental Crit (I'm not sure this is used/exists)
- +Physical Power(2)
- +Spell Power(2)
- +Mental Power(2)
- +Resource limit (mana, stamina, vim, positive, negative, ...)
- +Physical Saves(2)
- +Spell Saves(2)
- +Mental Saves(2)
- +Health
More leveling rewards
I'd like to see carry limit get a bonus on level up, instead of through strength investment. It's a natural move, in my opinion - the higher your level, the more equipment you have found (and want to have on hand). Equipment requirements, if they exist for the sake of balance, should just be relegated to level limitations.
Clearer definitions for immunities and saves
Saves currently seem to do everything and nothing. Removing up to 50% of an effect isn't too useful if that effect is already 30 turns long, nor does it mean much if that effect is going to get canceled by other means. Saves were changed back to allow the "shrugging off" of effects, which is a huge increase in effectiveness (trying playing the advanced tutorial in 36!). Immunities lead a troubled existence, being simultaneously way too good and not good enough.
It would be better for these functions to be more clearly defined. Immunities should only govern the complete resistance to (aka failed application) of status effects, and, where appropriate, acting through these status effects (confusion is all that comes to mind; perhaps also silence?). Saves should not reduce duration directly, nor should they allow the player to completely resist status effects. Instead, saves should allow the player to prematurely shrug off status effects on their turn, checking power against save to see if the effect is ended early. Status effect duration would then follow a geometric distribution.
Accuracy and defense should be a function of equipment
If accuracy/defense checks are meant to follow a very strict scaling (i.e. absolutely no chance of hitting over a certain margin), make them equipment-dependent. Armor and weapon choice would be much more important if the player could adapt to these situations. If defense was penalized by heavier equipment, there'd be greater reason for combat-oriented classes to wear light armor over heavy.
What I will say is that I don't really buy into the "role-playing" aspect of ToME - it feels more like a hack-and-slash turn-based adventure game with a lot of RPG/roguelike elements. Strength obviously would determine encumbrance if we're talking about real life, though the realism of carrying around a few suits of armor and a dozen weapons is questionable. I'd be curious to know how you feel about the transmogrification chest, since it really dodges around that fantasy trope. I don't quite follow your point about my system allowing you to subvert statistics; maybe I wasn't clear enough. I'm not saying that it's bad to stack a stat, I'm saying it's bad to stack it just so you can invest in a talent/equip a piece of armor. You are right in saying that a lot of these changes can be accomplished through changing how the current stats work.