Going for a happy medium between 3.5's skill points and 4e's single-stop proficiency might nip this issue in the bud. The first time you take a level in a class (regardless of whether you have other classes already) you get all its proficiencies and can select as many skills as normal. However, these things don't apply to all character levels universally, they apply only to levels in that class. So if you are a Ranger10/Druid10, you would generally get the level 10 benefits of proficiencies that are in only one of those classes (say Stealth and Religion) but the full 20th level benefit from the ones that are in both (like Nature). The same for the "core" proficiencies like weapons and saves. For example, the ranger has proficiency in all simple and martial weapons. The druid is proficient in a list of specific weapons, but they're all either simple or martial. So one would get the level 20 proficiency bonuses for druid weapons, and level 10 bonuses for all other simple and martial weapons. Level 20 saving throws in Wisdom, level 10 in Dexterity. Armor proficiencies don't yet fit into this scheme, but they are already the exception to the normal proficiency rules, and could probably use a rewrite.
Since one makes these proficiency choices exactly once for each class, the complexity of tracking it all depends directly on how much multiclassing one does. In other words, all the complexity is opt-in. A single-classed character's proficiencies are no harder than those in 4e, and unless someone takes a new class every level it is always simpler than 3e's skill points.
Proficiencies from Background, Race, and probably other non-class sources would still apply to all character levels, just as they do now. Besides being simple, I thematically like how those elements are effectively infused into whatever classes the character chooses to take. Race and background are highlighted as special, and they also exert some soft incentives on what kinds of multiclassing are easier or harder for that particular character in a way that feels much more organic to me than, say, 3e's favored classes.
Finally, make sure there is a way to make sure one can incorporate a proficiency into another class. For example, incorporating "Stealth" into one's Druid skills, and therefore calculating its proficiency bonus from levels of Druid as well as Ranger. It would be the perfect place for downtime-training, in my opinion. Simple multiclassing that results in full proficiencies for everything the character cares about might be relatively cheap. However, a character that takes 6 classes and has some level of proficiency in 15 skills would find getting full proficiency bonuses for each of those prohibitively expensive, and would need to concentrate on a few. It might even make a better check on multiclassing than the ability score requirements, although I'd need to think more about that.
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