Then a caster would have the same DC for every spell - as someone on the PF boards pointed out, what's the point of casting hold monster if hold person has the same DC? Especially if SR no longer applies?
The point is what the spell can effect. Hold Person affects only a specific category of creatures while Hold Monster gets just about everything else. That's the point.
The idea behind the alternate save formula (10 + 1/2 caster lvl + stat) is that the power behind the spells is based on the caster, not the spells themselves. Otherwise, lower level spells become 'throw-away' spells that don't really get used against someone and basically encourages casters to dump all their powerful spells right off the bat because of the DC rather than whether the spell is actually appropriate or not. It means that the 20th Wiz casting spells is going to have save DCs the same whether its a Fireball or a Meteor Swarm.
If you want to run SR as a bonus to saves rather than a separate roll, you could adapt a variation of my original suggestion on SR: Minor, Moderate, Major and Full SR.
Minor = +2 bonus/DC +6
Moderate = +4 bonus/DC +3
Major = +8 bonus/DC -3
Full = +12 bonus/DC -6
The bonus could apply to saves or AC, depending on the nature of the magical attack. For saves, they get the listed bonus to their saves against magical effects. If their save equals or exceeds the DC listed with their resistance, their SR works and they suffer no effects from the magic. In the case of Major or Full SR, they make their save if they hit the DC modified as above and SR kicks in if they make the original DC of the magical effect.
For AC, increase the target's AC by the listed bonus, if the attacker hits the 'normal' AC, his attack hits, but any magical effects, must hit the 'magical AC' provided by the SR bonus, or the target is not affected by the magical attack.
In the case of magic that doesn't offer a save, give them a save with the SR bonus in place of their normal save bonus.
Example 1: Lightning Bolt (DC 20) vs. target w/minor SR (+2 save bonus/SR DC of +6).
Target makes a Reflex save with a +2 bonus for his SR. If he makes the DC, he takes 1/2 damage (as normal) for the spell. If he beats the DC (20) by the amount his SR allows (DC + 6, or DC 26) on his save, then he is unaffected by the Lightning Bolt.
Example 2: Cleric with Major SR being attacked by enemy with +2 Shock Longsword. Cleric AC is normally 16; SR AC is 24.
The attacker must hit an AC of 16 to hit the cleric with his weapon. To affect the cleric with the Shock property of his weapon and the magical enhancement bonus, he must hit an AC of 24. On a 15 or less, the attacker misses. On a 16-23, the attacker hits and rolls damage, but does not include the damage from the +2 enhancement of his weapon or the Shock property. On a 24+ attack roll, the cleric suffers the normal damage of the weapon, the +2 enhancement to damage, and the damage from the Shock property.
Example 3: Target with Full SR hit by a spell that does not grant a saving throw.
The character uses +12 (his SR bonus) as his base save; with all other modifiers added in, he has a +20 save modifier. The save for spell is calculated as if it normally granted one (10 + 1/2 caster level + stat), and in this case that happens to be a 30. The character makes his saving throw if he gets a 24 (DC -6), suffering half the normal effects, but if he rolls the original DC (30), then he is unaffected by the magic, protected by his SR.