Sorry, I misunderstood you then. I suppose I hadn't accounted for DMs being just bad. I was exclusively talking about doing it right.
As to CR... a high-OP 2nd level party with 2 bfc wizards and 2 druids can likely handle many threats above their CR, but will have a much harder time with a shadow than a 3rd level party with a dread necromancer, or fighter with a magical weapon, who can likely deal with several.
In a party with no AoE, a horde of creatures is much more of a threat than it is to even a lower level party with a blaster wizard / zombie dragon / etc.
The actual party composition, capabilities, and tactics greatly influence just how challenging an encounter will be.
Or at least the option to chase down rumors of specific items.
Having bigger numbers lets you handle bigger threats. Having smaller numbers means you have to deal with smaller threats. If you want to modify your game to ignore WBL and not give out items, you need to have the party facing smaller threats.
Those first 3 can be solved with a ranged weapon anda bag of flour/marbles/caltropsplayer skills. I'll grant the 4th one, conditions that you need to fix, does mandate some expendable items and/or some casters. Because you can't just "get better" from being turned to stone.
Here, Wish is a quest-specific McGuffin.
And one you should never need, as any reasonable Illithid Savant has already procured the Tarrasque for its delicious regeneration.
Quest-specific McGuffin, ranged weapon, "yo, sage, where the portal be at?", numbers, agreed.
Protectingthe fighter from mind controlyourself from the fighter is, from your description, simply a matter of numbers. Thus, my suggestion of fighting lower CR foes covers this problem.
It is difficult to heal the only healer in the party without items. Go team cleric!
... Can everyone in the party handle an encounter by themselves?
If not, then you have a balance issue, not a gear issue. If so, then you have a balance issue, not a gear issue.