Where do I say it's "worth it" to take 2 malachite gems over 2 skill points?
In ED, I suggested to go with Wesson, because Radcliff only gets you 1 Skill Book instead of the 2 Wesson does. On top of that, if you choose Radcliff, you can trade his gem away for 2 Malachite Gems, at the cost of the single Skill Book he rewards. So in that case, you'd either choose Wesson for 2 skill points, or Radcliff for 2 Malachite Gems, but I always try and leave that decision up to the player, although in most cases I'll say the skill points are more valuable. The benefit level 10 enchantments offer over level 9 aren't worth 1 skill point in ED, so you only need a few Malachite Gems, really, and if you want enough to enchant a lot of stuff... I'd call it a waste.
In DKS, Radcliff gives 2 Skill Books (same as Wesson) regardless of whether you do the trade for 2 Malachite Gems or not, although that trade still denies you both upgrades to the Workshop.
You'll have to point out exactly where I suggest getting 2 Malachite Gems is more valuable than 2 skill points. In any case, Sight for Sore Eyes definitely gives 2 skill points, and has in all versions of the game.