First off, if you are unaware of the issues surrounding charms, marco wrote up a post about them.
With that out of the way, this is my attempt at a semi-elegant fix for the system thrown together in my spare time. It isn't perfect, but it isn't the current system (so it is probably an improvement).
The Core Idea
As the title suggests, the solution I have come up with is to turn the Uber Charms into glorified mystic orbs with the following modified properties (confirmed largely[/edit] possible by Quirinus in a brief discord question barrage).
1. Only one Uber Orb can be applied to an item
-Using the same Uber Orb rerolls the given stats
-Using a different Uber Orb removes the previous bonus and applies the new one
-Bonus is not doubled on Shrine Crafts/Honorific items
In the event that rerolling the stats from an Uber Orb would reroll the entire item as well (and it is decided that it would make perfect items too easy to acquire)
-Using an Uber Orb prevents further item modification (so find a perfect item, hit the lucky bonus, the get lucky with your uber roll... no problem)
2. Uber Orbs do not increase the required level of the item
3. Terror Difficulty can drop Slightly-Uber Orbs. Same deal, same mods at half values. (for if players are struggling, not strictly part of the plan, but nice for newer players)
Addressing the Problems with Charms
Dependency - Necessity
Not all charms are required anymore! You only have 9-10 usable gear slots, this means you can only have that many Uber Orbs in use at a time. Some people may even use the same orb 10 times further reducing the need for all charms.
This does however hinge on Orbs giving stats that aren't required to survive such as damage reduction or max res and as a result being seen as a requirement for use with all builds (resulting in a shift from needing all charms to 10 of one)
What build can beat all ubers?
if your build can beat all ubers, great. sell the orbs. But the only ubers you really need to be able to beat are the ones for the orbs you desire. Without the need for all charms, it allows for players to make characters dedicated to various orbs or sets of orbs or making a generalist farmer that isn't terribly fast in order to gear up more niche builds that take on the hardest content.
the sheer reduction in available stats means that item stats become more important again. Charms can fill out stats you are lacking, or provide stats that your gear would not otherwise enable.
Unwanted Skill Scaling
If you want +20 to all skills, it might be possible, but you'd be sacrificing all your other potential stats. At this point it is a high risk high reward option given you will not be able to portal cheese ubers anymore.
Unwanted Stat Values
Want to remove your strength and dex requirements from gear? go ahead, but you'll be sacrificing other useful stats.
Example Uber Orbs
Cube with a piece of Armour to add the following bonuses
All Resists +(11 to 20)%
All Stats +(20 to 30)
Increased Fire Damage +(15 to 20)%
Soul of Kabraxis
cube with an accessory to add the following bonuses
All Skills +(1 to 2)
Hammer of the Taan Judges
cube with a weapon to add the following bonuses
two handed weapons receive double the value
+(15 to 30) minimum damage
+(20 to 40) maximum damage
10% chance to open wounds
It feels weird to have to say this, but not all ubers need to provide an uber orb?
some zones have a drop bias already, this can be expanded.
items built from uber bits
other cube recipes requiring swirlies from the uber kill
There are also weird bits like the LC1/2/Ennead/BRC that need to be addressed as they do not fit into this system well as of yet, if the challenges can become character specific flags it means that characters actually have to do their challenges (rather than just buying/muling the charms)
basically charms are dumb, they were in vanilla D2 and they are only slightly better in MXL, this is one way to expand the system, but there is a lot of design space to be explored.
+max skills of which there are now 7? on charms would need to either die in a fire (meaning more skill point distribution) or find a new place to live.
in a world where we now level to 125, +1 could be awarded for each level past 120. giving a total of +5.
Alternatively a number of ubers could give it through their recipes (as a character specific stat)
Some charms could continue to exist - get a class charm and buff it throughout the endgame) with +exp gain and +max levels