I think the changes are a mixed bag and depending on the situation are either a nice bonus or a really bad deal. I'm assuming the new bonuses only apply to spells where SR applies. If it applies to all spells, there is nothing good and you should go back to RAW.
SR is usually set at CR + 11, giving a flat 50% miss chance for level-appropriate monsters. Against saves, spells land 25% to 75% of the time, depending on the save targeted. This makes SR spells land 12.5% to 37.5% of the time. This doesn't really change with level.
Your GM's new method varies with level, since the flat miss chance is now a bonus to saves that progresses every 4 levels. What that does is makes spells that target a strong save fall into 5% success range (Nat 1 to fail). At the same time, spells that target a weak save start out at a 60% success rate (at 1st level) and fall to a 35% success rate (at 20th level) with the break-even point around 18th level. So, at lower levels with you targeting the weakest save, the new method rocks (except there aren't many SR monsters at low levels, d'oh!). Otherwise, you're better off with RAW.
Spell Penetration is likely a wasted feat with the new method, as anything that increases your spell DC by +1 has the same effect and applies to all your non-SR spells too.
I didn't run hard numbers on AC, but many of the AC-related spells are touch attacks and the better ones also have a save (Necromancy). The AC bonus is punitive and like saves, increases with level. At 1st, it is +6 AC. At 10th, +10 AC. At 20th, +15 AC. That is really steep for a 1/2 BAB character even if it is against touch AC. If the spell then has a Fort save (often a monster's best save), you'd probably do more good using Aid Another to give someone a +2 to hit.
If it were me (I play debuff-style casters), I'd "hate it too much" and go back to RAW.
TL;DR: It depends. New method is better at low levels and when targeting weak save. RAW is better otherwise. AC aspect is bad and gets worse with level. I'd say no to it.