Alright. Well they dont so much 'hurt' as just 'nowhere near as good as the other options' so they never get taken.
Many of these, in my games, are no longer even considered feats. They're provided as core mechanics, or have some other way to deal with them.
I'm inclined to think that this is a better option than feat points.
Weapon Proficiencies: They simply aren't worth a feat. Even when they're giving you massive amounts of weapons, they just aren't useful enough. If you want to play a wizard who has a scythe, fine. But youre not likely to give up a feat for it, and I wouldn't blame you.
I agree that they are usually not worth a feat, but generally not for the reason outlined. A weapon proficiency feat is generally worth +1 damage on your attacks. If I had a feat that said, "You do +1 damage with a weapon.", people might consider it slightly weak, but quite possibly some would take it. The real problem with the weapon proficiency feats is two-fold. First, if you want to engage in combat and don't have access to good weapons, its far more efficient to splash a class than it is to spend a feat. And secondly, if you are planning to go into combat with weapons frequently, chances are you already are proficient in virtually all weapons and don't need to spend a feat.
All that indicates that they aren't really worth buying, but I'm not sure that it means that they aren't 'worth a feat'. As I said, effectively they give you +1 damage on your attacks. The clerical 'War' domain gives you martial weapon proficiency and weapon focus for 'free', which effectively means '+1 to hit and damage'. That martial weapon proficiency is no less useful to the cleric than the weapon focus that SKR touts so highly, and no less valuable to them.
(Weapon Profs aren't feats anymore in my games. I have the player 'practice using the weapon' and after enough check rolls have been made, the player can use the new weapon, mid level. Every so many BAB I let the players just gain a new weapon group (UA Weapon Groups))
Do you do the same thing with spells? Maybe let a fighter pick up a few 1st level spells by practicing with them and gain a new one every few levels?
I'm not fully happy with the weapon proficiency system, but I've never seen a really nice non-abusable system that addressed all my concerns (similarity of weapons, no ethnic bias, balance, not yet another thing we are giving casters for free and then complaining that they seem overpowered).
Eschew Materials (Components under that cost are usually just assumed to be in the player's possession anyways, and people usually just don't use components unless theyre really pricey.) Even if you tediously track components, it would be easier to just buy a stock of components instead of using a feat on this.
Again, the problem with this feat is that in most campaigns, you get it for free, which adds it to the category of 'yet another thing we are giving casters for free'. Still, I agree with you that this is somewhat suboptimal and generally only really comes up if you've been imprisoned or otherwise lost your possessions.
Run if only useful if youre using third party chase rules, as in standard D&D, if 2 creatures have the same speed, they'll never catch eachother.
I'm not sure I follow. Chasing in D&D according to the RAW is wierd because you have to plan it far more carefully than is reasonable (usually with some sort of overrun or overrun trap depending on how your read the overrun rule), but run certainly changes your speed and allows you to 'catch something' or just as importantly to get away from things that would otherwise be faster than you. However, I tend to see this primarily as a problem with the rules regarding chasing, not with the value of being able to run faster. Another probably even bigger problem with the Run feat is that most DM's seem to make all their encounter distances 60' or less. If you've got encounters starting at 400' or more with some regularity, then the ability to cover ground becomes more important.
3.5e Toughness was worthless.
No. 3.X Toughness didn't scale, but that doesn't make it worthless. It turns it into an NPC feat. At low levels of play its one of the most powerful feats in the game. The problem with it is that since it doesn't scale, its utility diminishes the longer that you play. There is a simple fix here though. If the feat doesn't scale; make it scale.
There is another subtle problem here with Toughness, in that unlike Dodge, Power Attack, and Combat Expertise, it's not a 'gateway feat' that opens up alot of powerful options to you. IMO, it should, allowing you to build a 'toughness' focused character the same way you build a str based power character or a dodgy dex based character.
You're already spending your feat on it, the xp you have to drop on items quickly adds up, making you lag behind in the group, usually for items that are consumable and are by this time worthless. Unless I need to make a unique superpowerful item for myself in secret (Possibly to turn myself into a lich or something), I'm always better off buying it or hunting down a wizard and hiring him to make it.
Again, this isn't a problem with the feat. I know for a fact that if you don't make magic ideas readily purchasable that the item creation feats suddenly become hugely important. Obviously, just as in the real world, if you have readily available consumer goods, the ability to craft and create things yourself quickly diminishes in importance. If you don't have that, then the ability to craft and create becomes one of the most powerful and necessary of all skills. Arguably, making magic items freely available constitutes yet one more thing with are giving casters for free.
Metamagic Feats: I'm already paying for this once, by buying the feat. Usually, it's not worth the effort to even take these, because the higher spell slot makes the spell less useful, and because you had to know you needed it in advance. If metamagic feats were spontaneous to everyone, they would be useful.
Limited utility, I agree, but Wizards generally get a couple of these for 'free'. I've rarely seen more than 3 or 4 spells on someone's list be metamagiced. However, this doesn't necessarily prove that they aren't 'worth a feat', as they are situationally quite useful and virtually all the monkeying around I've seen with them results in something clearly broken. And much like 'falling' I don't think 'silenced' or 'constrained' should be considered an unexpected event.
I'm not sure that 'quickened silence' would be any better than just 'silence' though as a 'counterspell', as quickened does not turn a spell into an immediate action. Maybe I don't understand what you mean.
Plus, feat-trees. Often, you end up having to take feats along the way, which you will never want to use. I've had this come up with Power Attack/Cleave before. Cleave was useful for a character, but power attack was useless, so cleave actually cost me two feats. That's just an example though.
Yes, it is, because 'Power Attack' is one of the more powerful and useful feats. Granted, in 3.X they managed to find a way to make it simultaneously less useful (in that fewer concepts could take advantage of it) and more broken (in that for those that could, it became even more powerful), but you are going to have a hard time convincing me of this argument using this example. I've a hard time imagining Power Attack ever be completely useless though. I will say that often I've seen feats created that are deep on a tree or have other significant prerequisites for no good reason. I will conversely say that I don't think feat trees go deep enough, and that fighters in particular need some even more powerful feats deep on feat trees for the sake of balance.
