And yet, it also allows for a natural gradation in levelling. Perhaps it would be better if the skills were linked, so that rifles were prerequisite for assault weapons, say, and pistols for beam weapons?

This is a little like Torchlight, where later skills and spells have quite different effects (in broadly similar categories, like magical shields and summons) typically with different classes of damage, fire, ice, etc.

There is a difference; in a typical skill point system, if you spend a lot of points in an early-game skill, you won't have enough points left to get good at a late game skill in a reasonable amount of time. Wasteland, with skills increasing through use, is not like that; even if you invest heavily in early game skills, you'll still have enough of an opportunity to level up late game skills to the point where they're useful in the end game.

I don't remember whether I mentioned it, but there are some games where the damage formula is different for different weapon types. You see this in some SaGa games (most notably SaGa 1 and 2, as well as SaGa Frontier), and in Final Fantasy 5 (but not other games in that series); this diversity of damage formulas means that different weapon types might work better for different characters or situations. (For example, in FF5 axes pierce defense and have a lot of damage variation, making them great on high defense enemies but not so good against weak cannon fodder (because you might get a low damage roll or miss entirely), while in SaGa Frontier gun attacks use the WIL stat, which is also used by magic, making guns the best physical weapon type for magic users.)

My point was to use the earlier skills as prerequisites, or perhaps a bonus, for later skills.
As long as the correlation is not too abstruse I see no problem with different damage depending on the situation, opponent and protagonist. So a large mallet might have difficulty actually hitting a mouse (missing most of the time due to the rodent's superior dexterity) yet still squash one should the gamer luck out and connect.

But the reason for the difference needs to be credible, or it will detract from the fun of the game.

Another example is UFO: Aftermath, where there are three types of ammunition, hard, soft and other, which are optimally applied against armoured and bloated enemies. So, for instance, FMJ rifle rounds will certainly pierce the flesh of a caterpillar-like psionic opponent but softer ammo will devastate it better, whilst softer ammo will tend to careen off hardened plates. The game also deploys different categories of protection (against inertia, energy, psionics, etc.).

edit: categories of defence

One of the best changes the DS remake of SaGa 2 made, at least for someone not as familiar with the game mechanics as I am, is that the game actually gives you part of the damage formula for weapons, including the stat and multiplier. Hence, it becomes clear that Rapiers do their damage based off AGI rather than STR. Of course, it still takes a bit of thought or experimentation to come to the conclusion that equipping a robot with a whole bunch of them would be a good idea.

On the other hand, the ChainSaw's exact mechanics aren't so obvious, though in SaGa 2 having higher strength will allow you to saw apart more powerful enemies. (In SaGa 1, it's the reverse.)

Final Fantasy 5 doesn't have as much stat micro management, as any character with the same level, job, and secondary ability will have almost the same stats; on the other hand, the variation of damage formulas still allows advanced players to come up with interesting set-ups to maximize the effectiveness of less conventional weapons and spells. (Don't forget that FF5 is the FF game that introduced Blue Magic, which has many spells with unusual mechanics, like using the caster's HP in the formula, or Goblin Punch acting like a physical attack in some ways, but still having unique properties.)

This works well if the elemental resistance and weaknesses are logical, and there isn't some easy way to work around this.

Phantasy Star 3, for example, does this wrong; enemy resistances don't have an obvious pattern, and in most cases physical attacks, which aren't affected by this, don't have that issue. (With that said, there is an interesting dynamic where most physical attacks are affected by enemy defense, but Wren's attacks are not, so it at least has something there. Plus, there is a technique that can cause instant death and is actually useful and cheap.)

There's also situations where you need to choose a specific type of damage to focus on, or a specific type of damage to take with you into a dungeon, and without extensive knowledge of the game (or very good hints in at least the latter case) is not a meaningful decision for the player to make. (I've encountered this in Lennus 2, where early game your main character can only have one element available at a time, and the game has elemental symmetry unlike the first game in the series.)\

There is added benefit of permutations, too, whereby a particular type of armour may protect the character more from one category of damage and less of another, with some having obvious weaknesses and strengths, whilst others have better all-round protection.
Underdark, the second expansion of the original Neverwinter Nights (and by far the best of the entire game) takes the player into a hell or two, and if you haven't taken the correct precautions (against a particular elemental damage) then the task is that much more difficult (with ambient damage from the elements during non-combat perambulations, just like the earlier Icewind Dale games' encounters with salamanders).

Some RPGs will give a lot of information about a weapon's stats, but neglect to explain why one should pick a mace instead of a sword with identical stats, for example. Too much info will disincentivize experimentation, making it less likely the player will figure it out on their own.

Reminds me of Final Fantasy 5's Flame and Coral rings, which give you some elemental resistances, but also come with a weakness. Bone Mail is similar, and provides the highest defense of all armor, but it also gives its wearer Undead type, which is usually not what you want. (Undead type has some advantages, but seeing as most healing will hurt the character and resurrection will fail, you don't want the effect unless your set-up revolves around it.)

The other issue that discourages experimentation is when the game system is designed to lock the character into a single type of weapon for the entire game. If you have to stick with a single weapon type, then you can't really experiment with different weapon types.

This is one of the reasons I dislike skill point systems; the weapon proficiency system in the Baldur's Gate games and Icewind Dale 1 also have this problem (and it's actually worse in Baldur's Gate 2).

your initial post foregoes the whole point of melee weapons used in a fight, not to mention the fact that baldurs gate does contribute slash, piercing, blunt damage factors

But, without knowledge of the game, how do you choose which damage type, seeing as the proficiency system forces you to make a long-term choice right away?

(It wouldn't be so bad if you were automatically proficient with every weapon your class can equip.)

Yeah, that's the ticket. :)

Fallout had a leather jacket with different protection (against laser scorching, elements like fire and inertial forces like firearms) than the leather cuirass and the hermetically sealed atmospheric drysuit of the brotherhood.

Planescape have factional significance, too, with uniforms for members that bestow some benefits.