As for Armor, I think I'd just ditch having stat modifiers there. You can beef up your AC by getting heavier armor or better enchantments. Just leave it at that. You're a rogue and you want to be mobile and wear leather? OK, fine, you'll be somewhat easier to hit, but so what? You can have some 'dodge' ability or something that you can pick up, which the big clunking guy in plate isn't going to need. The range between unarmored and plate just won't be all that big. The suggestion of fewer armor steps is good too, and goes with this. SImply have None, leather, chain, scale, plate. Wearing plate is good for 5 points of AC more than the wizard with 'none', and that's just about perfect. I'd basically have one proficiency that let you wear the 3 heavier armors, and keep the small armor penalty as well and just apply that to the 3 heavier armors as well (this stuff can be tweaked).
For armor, I'd like to explore a concept of:
None: AC x+4, damage resist 0
Leather: AC x+3, damage resist 2
Chain: AC x+2, damage resist 3
Scale: AC x+1, damage resist 4
Plate: AC x, damage resist 5
The PCs in low or no armor dodge better, but get hit harder if they get hit.
Say that the D20 die roll required to hit None is 13 for a given foe and the die roll required to hit Plate is 9 and say the foe hits for 10 points of average damage.
Average damage becomes:
None: 4
Leather: 3.6
Chain: 3.5
Scale: 3.3
Plate: 3
So overall, the heavier armors protect slightly more. But, the PCs in heavier armor also get hit more often as well.
A higher level foe that hits easier +2 and harder +2 would result in average damage of:
None: 6
Leather: 5.5
Chain: 5.4
Scale: 5.2
Plate: 4.9
Combine this with Dex adding to AC, but not to hit for melee. Str is used to determine to hit for all melee classes.
The concept that any ability score can be used for to hit and damage in melee (and any ability score can be used to boost AC based on class) seems off to me. Just like Wis or Cha add to Will and Int does not, ability scores should be specific as to what they modify and this shouldn't change from class to class.
Magic armor could then add +1 to the resistance that the armor supplies and nothing to the AC. By definition, it would protect better and not just by random chance.
Another aspect of the game that this helps to alleviate is the swinginess. I've played (very high) AC defenders where the DM often rolled out of his butt. So, the defender got hit often not because he had more foes around him, but because the DM dice were hot. Lowering the chance to hit via AC doesn't necessarily equate to lowering the overall damage that the PC takes.
But, lowering the damage via resist automatically does, at least for any single attack.
In the first example above, a Defender in resist 5 Plate with 30 hit points has to get hit 6 times for 10 points of damage to go unconscious.
The Controller in resist 0 no armor with 25 hit points has to get hit 3 times.
This makes sense to me. The guy in armor is much harder to take out because the armor absorbs part of the blow each time. That's the reason armor was invented. Not to make a person harder to hit.
If a player wants to avoid the swinginess, he would move to a heavier armor. If the player wants to play the odds and hope to not get hit, he would move to a lighter armor. With the randomness of a D20 in the current game, heavier armor will typically help in the long run, but doesn't necessarily help at all in the short term.
It's great that you have armor on, but it's not helping in this encounter.
When I see Iron Wizards floating around who have high ACs and get hit on average the same as a guy in Plate and they don't really get taken out that much quicker if they are hit, just because they are smart, it doesn't make a lot of sense. Armor doesn't appear to protect that much. Adding Int to AC is purely a game balance rule. It really doesn't make sense that a low Dex high Int character is really going to be smart and experienced enough to dodge blows as well as a high Dex character.
Risk and Reward. Today except for Strikers, most PCs can do similar amounts of damage and can have similar levels of defenses. There is less of a concept of the lowly Wizard in the back that avoids direct combat because he is so frail, but he gets other significant advantages. Sure, he can slow a foe. Not that this helps that much.
Any more, that Wizard can have defenses as high as other PCs and the only main difference is that he often has fewer hit points (and part of that can be alleviated with Toughness and good Con or backgrounds). Wizards are these mighty warriors that can wade though combat just as much as the PCs in heavy armor, well protected by, err, their intellect.
Course, changing the armor this much is extremely not D&D-like.
Alternatively, having shields give damage resist instead of AC might be an option as well.