RPG systems are complicated and an have unexpected and unanticipated reactions with each other, and especially in a game with as much freedom to build a party as DOS 2 offers. Balance is not really something you can get perfect on your first attempt. You say that you think Dos 2 is an "absolutely excellent game", but it did not start out like that, unchanged from the first iteration. What you call excellent is the result of thousands and thousands of small balance changes, the majority of which the players never even knew happened because the developers caught them in design, testing, and internal implementation without the players ever getting to see them.
"Making all skills the same" is a strawman argument which no one is suggesting. An RPG should have a variety of viable approaches to a situation, and making sure all skills have some reasonable use is a good thing. Skills can be quantified in DOS 2, because all skills use 1-4 AP. Regular attacks cost 2 AP, most damaging skills cost 2 AP, high-power skills cost 3 AP, really high-power Source skills cost up to 4 AP. Physical skills are described as dealing XX% of weapon damage. This makes it fairly simple to do total damage per AP calculations. This is a simplification, because many skills have extra effects which could be more (or less) useful depending on the situation, but it's a good place to start when comparing skills.
For instance, take the Huntsman skill "Assassinate". It costs 3 AP and deals 115% weapon damage, with an additional 50% for attacking while in stealth. 3 AP is 1.5 standard attacks, so for the skill to break even, it should deal a total damage of 150% weapon damage. You could use it from outside combat for the extra 50% damage, but that costs 0 AP, so it doesn't count. 115 is less than 150, so therefore using Assassinate while not in stealth is not worthwhile. (If you only have 3 AP left, you'll need to whip out a calculator to be sure you can kill an enemy even on the low end of the damage range.) So that brings us to the case of using Assassinate while Stealthed. We'll only talk about the in-combat use, because out-of-combat is free. Chameleon Cloak or a potion cost 1 AP, so Invisibility + Assassinate costs 4 AP. Sneak costs 3 AP, so Sneak + Assassinate = 6 AP. 3 regular attacks deal 300% damage, so that is the break-even point for Assassinate. However, whether the sneak bonus is additive (115 + 50 = 165) or multiplicative (115 * 1.5 = 172.5),the result is still less damage than 2 normal attacks (200%). Therefore, the skill Assassinate is not worth using in combat unless the base damage were to be increased from 115% to 150%.
Unfortunately, the problem is complicated by that the freedom to flee combat and return means that buffing Assassinate's in-combat effectiveness will also buff it's out-of-combat effectiveness and allow it to be exploited by running away while the rest of the party is in combat, coming back in Sneak mode, then Assassinating again once the cooldown is off. This skill is balanced around the possibility of it being used outside of combat.
You talk about having some powerful unique weapons which have a high cost or take a lot of effort to get. DOS 2 has the weapon Anathema. To get that you need to complete two quests in Reaper's coast to find it, even then it takes a long time before you get your hands on it, Tarquin has to stay alive the whole time, and when you get it, it's a piece of junk. It can only be used once. It's intended to be used on the final boss as a big mega-damage ultimate weapon. It's been built up all game, and it barely does anything to him. Considering the AP cost for switching weapons, it's possible that it's actually LESS useful than sticking with your original weapon and never using it at all. That is a balance issue, though, so by your rule, it should not be fixed.
