Well Editor, here's how I see things (from the point of view of a once control engineer):
Ultimately, as a character levels up, they should get better at what they do.
As it stands, some classes get better at hitting than others.
Some classes get better at using magic than others.
All classes get better at resisting these forms of attack equally.
In order for the steady state of the game to be fun and playable, these three factors have to increase in equal amounts. That's fine. The problem lies with the available 'offset' boosts, not derived from level. In the case of armour and effects adding to reflex save, there's an offset that with 3.5 numbers, far outweighs the offset you can apply to BAB. But you need armour for the game to have the spirit of D&D.
So imagine if you include recommendations to restrict magic items. Make the cost of adding a to hit bonus to a weapon the same as the cost of increasing the AC of armour. Make magical bonuses to armour the same effect as rings of protection, so they don't stack. Similarly with magical bonuses on armour and a shield - just make all the +1, +2, etc.. deflection modifiers (or even better, magical equipment modifier). Suggest the same costs and limitations apply to skill boosts, as even in 3.5 some items are ridiculous.
So now if we assume that any magical bonuses to reflex are complemented by equal-costing magical bonuses to weaponry, the only offset to worry about is base armour. At first level, in 3.5 also, AC is usually higher than to hit, and we don't complain much about it. As the Fighter progresses, he'll get +1 to hit every level, where reflex defense only goes up +1/2, with perhaps some improvement from the type of armour being worn. But in essence, we've taken a problem and distilled it down to one that already exists in 3.5. Sure the Wizard is gonna suck at hitting, but that's why they have magic.
Now for magical attacks. Using caster level will be the same as using BAB vs. reflex for Fighters, but there are almost no magical bonuses to it. This is where I think the idea of using spellcraft actually works. At first level there's a +5 offset at most, but as all parties concerned level up, basic armour will add to reflex and fortitude. Magic bonuses should again cancel out in terms of cost. Taking prestige classes and multiclassing will offset defenses. But essentially, the skill and the defenses increase at the same rate, you need only consider if the offset is small enough to make this balanced. My thoughts are that even with skill focus in spellcraft, the +10 offset is equal to the full plate and shield combination. Adding spell focus style feats could tip the balance too far. Will defense is a problem too, unless there are ample ways to boost it from class abilities etc. (although many PHB will saves let you keep on saving, there are certainly few nasty damage spells, perhaps this can be extended to all). Perhaps a nice tradeoff would be specifying a school of magic for skill focus spellcraft (or dispelling if you don't want a school) - that gives the Wizard something to spend those feats on!
We need a playtest
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