It seems to me fix is to slightly deferinciate the types of "proficiencies" there are:
1.) If you get a duplicate weapon or armor proficiency, you don't get a bonus choice.
2.) If you get a duplicate tool, you can select a different tool of your choice.
3.) If you get a duplicate skill, you can get a different skill of your choice from your class list. (Note: this is hard since most classes give a choice anyway).
4.) If you get a duplicate save proficiency, you do not get another choice.
This would be a good start.
1.) Weapons and Armor. I agree, regardless of the source: multiple proficiencies should not be not transferrable.
2.) Skills. I've noted
earlier in this thread that there are currently two classes of tool proficiency: individual items (e.g. instruments), and classes of items (e.g. mounts). Multiple proficiency in the class that are individual items is not a problem. What is a problem is trying to gain proficiency in a whole other class of items. Indeed, I think this can go back to an issue in the playtest materials ten months ago, when tools were first introduced.
As I described then, tools were serving no purpose that was separate from skills. That's now come back here, and the problem is amplified because there are so many more tool proficiencies. Instead of proficiencies (mounts), re-introduce the
riding skill; instead of thieves' tools, re-introduce
disable device. Just because a skill requires the use of certain equipment (a horse, a lockpick, climbing gear), does not mean that there should be a bonus from that equipment.
In brief: Replace most tool proficiencies with a skill, and use the skill system.
3.) Skills. This is fine, with the following two caveats:
--> if the skill is granted by a feat (except Athlete and Loremaster), then you do not receive another skill. So, for example, Choosing the Alert feat if you are already trained in Perception does not allow you to choose another skill freely.
--> I would like all classes only to grant 1 skill. If there are to be more, then it should come as a class feature (as used to happen with, e.g., Religion and clerics). The advantage of this approach is that it opens up more design flexibility, while creating uniformity: (a) Bards can still receive expertise without necessarily receiving the attendant extra skills; (b) Bards and Rangers can be granted an extra skill at level 3, reducing the impact of level-dipping; (c) the extra skills of a Rogue can be granted, as in the very first playtest materials, as an extra (second) background -- either at first or third level. That gives skill (and possibly tool) proficiencies (and a trait), but allows rogues to be skill-monkeys while still only granting 1 skill by class.
In brief: all classes should give 1 skill only, and rogues should have a second background.
4.) Abilities. Save proficiencies are a problem, because they are going to be so useful, especially at higher levels. Perhaps should be limited to one-extra save proficiency if you multiclass, not (usually) two.