The Saving Throw issues

Well although there are many discussions on "oh my god some classes are penalized in every way" barely anyone tries to address the mayor reason why that's the case.

At high levels the gap between good safes and bad safes is pretty wide before feats or magic items. And if you compare some classes against each other (like fighter vs. cleric) you see some additional issues. A fighter has to raise his Strength to dish out more damage and cannot spend attribute raises on his poor safes to make them any better. On the contrary a cleric will raise his Wisdom and that will stack very fortunately with his good will safe.
Ok, both will then have a bad Reflex safe, but most spells with reflex to safe against are "take half damage", not "safe or loose/die for sure".

So now, is this really an issue? Yes it is. Simply look at the numbers of DCs for Special abilities and compare it to the safes. I left out MIs as that can be individual, but you can clearly see that a bad safe simply needs a +5 to safe boosting as item - and a +5 Item even to a safe - is expensive.
Also for special abilities I left out anything you might get from Classes or Feats as goodies.

DCs of special abilities (lvl 1 /20 /difference)

• (DC 14 / DC 16 / 2) - 0th lvl spell of a cleric (starts with WIS 18, max. raises)
  
• (DC 15 / DC 25 / 10) - 9th lvl spell of a cleric (starts with WIS 18, max. raises)
• (DC 12 / DC 23 / 11) - Stunning Fist of a monk (starts with WIS 14, 3 raises)

Safe Bonuses (bad /good ) at lvl 1 without items

• +4/ +6 - safe on primary attribute (starts with 18 in attribute, max raises)
• +2 / +4 - safe on secondary attribute (starts with 14, 3 raises)
• +0 / +2 - safe on other attribute (starts with 10, no raises)

Safe Bonuses (bad /good) at lvl 20 with a +5 safe boosting item

• +17 / +23 - safe on primary attribute (starts with 18 in attribute, max raises)
• +14 / +20 - safe on secondary attribute (starts with 14, 3 raises)
• +11 / +17 - safe on other attribute (starts with 10, no raises)
  

Well someone who cannot spend points on a safe attribute and has a good safe will only have a chance to be as good as one with a bad safe on his/her main attribute. You see the DCs usually raise as fast as a good safe. If you check some iconic monsters that are good spellcasters you'll get DCs in the high 20ies as well.
As the last case of safes shows if you go - and only if you go - the +5 MI route you have a chance to keep a bad safe in line with the DC of a level-appropriate Special Ability. In addition it shows what a deep impact a good stat has and what a raised or not raised stat has. It is pretty drastic.

So in my oppinion several things have to be done:

1. Increase the gain of safe bonuses in general
2. make the gap due to progression more reasonable
3. strongly reduce the impact of attributes on safes to bring classes that cannot afford attribute raises on safe attributes more in line with classes that favor certain safe both by progression and by attribute raise

What we need would be a bad safe that goes from +2 to +17 (if we factor in the +5 MI boosting item) and a good safe should go from +6 to +21 and this leaves us with two progressions of 1/2 lvl and 3/4 lvl - that's much closer as gap, but 25% success chance still a significant gap, but one that does not completely grant an almost automatic success to an attacker.

Attribute Modifiers on Safes
Well I toyed with the idea of lessening the impact of attribute modifiers to safes "just like in the old days". I think that would worsen the situation as it would invalidate a bit too much of the system.
The direct fix will address it well enough.

Resulting Bonus System
All Safes grow at a rate of 1/2 Level. Classes that have safe declared as good safe grant a +2 Class-Save-Bonus (CSB) to that safe and an that bonus increases by +1 for every 5 class levels up to a bonus of +5. Should multiple CSB affect a single Safe only the best of them applies.

If you multiclass into more then 3 classes and at least 2 classes grant a CSB of +3 to a single safe your CSB increases by +1 unless it already reached +5.