I wasn't even talking about the requirement to be sneaking when you use Garrote when I said it was a bad skill. It does I think 2 more damage than kick and silences for 1 second longer. You get kick at level one, and garrote at level 45. To me, 45 levels is worth more than an extra 2 damage and a second more of silencing. I wasn't thinking about the sneak requirement, but upon reflection, it is annoying that you have to be sneaking to use it, because if someone gets the first hit on you (which happens very often), you aren't sneaking anymore. If Garrote were actually worth any major amount more than kick, then the sneak requirement would be fine. However, as of now, it does hardly any more. If you can sneak up behind a person while using sneak, then great, you just got a garrote on them... 4 (5?) seconds of silence and like 9 damage... and like half of your stamina. It's really rather difficult to sneak up right behind someone in the open wilderness, though. Often you'll only do it successfully in an area with a lot of hiding spots. An open field doesn't really have that many. So, to get a successful garrote off in an area like that, you've got to use smoke so they don't see you when you use it, or you've got to use one to catch them before they can react. Both of those skills consume a ton of your EXP. If you use garrote with one of them, you are down to the point where you cannot even sprint.
That is my main concern with Ninja. With a melee class, you shouldn't rely a ton on skills, but you should actually be able to use them somewhat effectively. When it comes to Ninja, you cannot use two skills and still even be able to sprint. Ninja has 5 true combat skills; kick, blackjack, garrote, envenom, and eviscerate. It has 4 utility skills; one, smoke, sneak, backflip. You would probably start a fight in sneak though you probably wouldn't stay in it long enough to do anything with it, and you'd probably start with blackjack. However, if you want to use your utility skills to any sort of effect other than fleeing (and even that is difficult), you can't use a single combat skill in combat.
Heroes melee classes are mainly meant to hit the other guy a lot with a weapon. Vanilla melee classes (class singular, actually; the standard Minecraft player) are mainly meant to hit the other guy a lot with a weapon. The primary reason that Heroes melee and Vanilla melee are different is that Heroes melee involves skills. The main purpose is still to hit the other guy a lot, but you have some added bonuses. Skills are there for you to use, not to rely on. You are correct there. However, with Ninja, it is impossible to really even use skills at all. You can use one skill and still be able to sprint, pretty much. When you say not to rely so much on skills in combat with Ninja, you are basically saying don't use skills in combat as Ninja. So, if someone is to use the class based off of that, it might as well just be a crafter class, because you'd only be able to fight with Ninja as vanilla.
Currently, when it comes to combat, Ninja is a pretty bad class. Ninja/Thief and Warrior classes are similar in that they are both melee. Some Warrior specs may not have too many skills to use in combat, I guess, according to what you are saying (although I've fought pretty much every Warrior spec except Paladin, and my screen is spammed with skill messages that aren't mine), but even if that is true, they make up for it with armor. Ninja/Thief are supposed to be sneaky high DPS classes. Thief is pretty good because it has many helpful combat skills (eviscerate, confuse, kick, backstab especially) as well as high-damage hits. It lacks heavy armor, but it makes up for it with the combat abilities (which it can actually use pretty effectively) and damage it has. Ninja has high sword hits, but it doesn't really have many helpful combat abilities when it comes to a fight with anyone other than a caster. Eviscerate has a 20 second cooldown and high stamina use. Envenom does a good amount of poison damage and uses like a third of your stamina, not too bad. Blackjack only works sometimes (rarely, it seems). Thief has backstab instead of garrote as a true combat skill (confuse just confuses them). That is helpful in any fight. Ninja's Garrote is only helpful (and that is a stretch) in very specific situations, generally only against casters too. Using it on a melee class will just stop them from using bleed on you or something.
You say that as a melee class you shouldn't rely a bunch on skills... If Thief didn't rely a lot on skills, then when Ninjas and Thiefs fought, the results would be much more level than they are now. And if Warrior (and specs) didn't rely on skills, they would just be the standard vanilla Minecraft guy who has a lot of armor. Skills are not the only part of combat by any means, but Ninja is bad because it cannot effectively use any good skills in a fight.