Okay, let's try again. I'll give examples of my suggestions.
• Increase in DT/DR of some resistance, for the player or NPC of choose.
Example1: At a certain Lockpick level (say, 85%), you get the chance to unlock a container. Inside, you find a combat implant. Some doctors can plant it for fee - on you, or on some of your NPCs - for +1 DT for all resistances.
Example2: At some Barter level (like 125%), you get access to a special item in a shopkeeper's inventory. There, you find some kind of a gel, which adapts the user's organism for electric damage. You can use it on whoever you wish, it has infinite charges. It grants 15% Electric DR and 3 Electric DT on first use and nothing on uses after that.
• Overall, any increase in anything (melee damage, HP, AP, etc.) will do. Just not useless bonuses like increases in Poison/Radiation Resistance, Carry Weight could also be considered useless, because it doesn't makes you any stronger, it just makes the game more comfortable.
Example1: After you have 115% Speech, you can convince some doctor to give you health advices. Boosts your HP. Also an option to boost your NPCs' health (and HP).
Example2: The San Francisco unarmed "trainers" (Lo Pan and Dragon) can train you for more Melee Damage - you need 150% Unarmed for your first training, and you get 3 Melee Damage. You get 4 more at 175%, 5 more at 200%, 7 more at 225%, 8 more at 250%, 10 more at 275%, and 13 more at 300%.
It's easy to say that in vanilla, Skynet and Cassidy are the top NPCs, followed by Vic, Marcus and Sulik. The Megamod isn't changing this a lot. The player should have a larger variety of joinable NPCs - it needs more melee NPCs (the dogs and Goris are weak), more NPCs capable of using big guns and energy weapons, more NPCs available to evil characters. In fact, the game needs an NPC available only to evil characters, because being evil makes you much weaker than a good character (not a purely good character, just enough to get the benefits from high karma). The ability for Doctor to change your NPCs' races, or to construct robots with Science could fix this, but the player needs to specialize in the skill to get these NPCs.
Example1: A gangster-themed NPC in New Reno, that hates "do-gooders". Uses Big Guns and Unarmed, also limited use of Melee Weapons. Good at taking damage, not very high Action Points (or possibly give him/her high Action Points, make him/her the best NPC in the game, because being evil really hurts your game).
Example2: Another Super Mutant. Much like Marcus, but with altered stats - different AP, HP, resistances, and melee damage, some of them in favor of other.
• Weapons unique in some way - like an energy weapon with 60-90 EMP damage and 5 AP requirement. I have ideas for a huge number of weapons. Anyway, most of them should be obtained by the skill for them (maybe also Repair), if you are going for that idea.
Even if the Megamod has enough weapons already, it could use more "unusual" weapons. AFAIK, still the only weapon that uses Fire Damage is Flamer (and Improved Flamer). Fire Gecko's Fire Breath doesn't counts. Also, see my previous post, and the things I wrote about the weapons (they are the examples). I could help you make some of them obviously balanced. There are truly different weapons. Possibly adding the aspect of changing your weapon (and your NPCs' weapons?) depending on the battle. Changing enemies' armor stats to be more like "0%/14 10%/2 85%/15 75%/20 50%/1 25%/4", or something like this, would help this a lot. Changing the armor's stats when weared by the player (or him NPCs) could further add pre-combat preparations. But that is another idea.
♦ Unique armors - they must be better than any other armors in the game in some way. Like an armor with high DTs and low DRs, or vice-versa. Or an improvement to APA Mk. II. Or armor with other SPECIAL bonuses, if you manage to invent the perk.
Again, what I mean is really a different type of armor, not something like Leather Armor Mk. III. I can help get it balanced, it's not that hard - just small bonuses above some armor. Or a bonus to SPECIAL, which can be compared by the APA.
Example: At 145% Gambling, gambling in NCR (near Duppo) after winning some money results in one of the players betting his unique Lucky Combat Armor, which has better protections than all forms of Combat Armor, and slightly worse than Power Armor. Also grants +2 LK.
Alternative: If you can't make it give +2 LK, instead make armor with protection slightly lower than Combat Armor's, Electric DR 75%, Electric DT 10.
• Improvements to something that could still be useful at the whole time of the game (mostly NPCs).
I really wasn't clear here (more unclear than I usually am). Basically what I mean is anything that improves you (or an NPC). I actually mentioned the most things that do it - like bonus HP, AP, Melee Damage, skills.
• Option of indefinitely trading something for something else (like Small Energy Cells for Micro Fusion Cells).
Example1: At 100% Science, you can convert 4 SEC to 1 MFC and 1 MFC to 1 SEC. At 175% Science, you can convert 2 SEC to 1 MFC and 1 MFC to 2 SEC.
Example2: At 155% Barter, you can change 1 .223 ammo for 2 10mm ammo JHP at some shopkeeper.
It's just a way to make it
slightly easier to manage your resources as bonus for investing in a skill. It's far away from unbalancing anything.
• Items similar to the +1 CH eyeglasses.
I actually had no ideas with this one. Items that have to be equipped for the player to benefit from them, like the Motion Sensor. Oh, forget about it.
• Bonuses similar to the ones I suggested to be granted by some of the skills (like the First Aid suggestion).
Just see my post about the skills and use something similar to the things I talked about there.
Example: Medicine that grants +1 AP for 24h contained in container requiring 85% lockpicking to unlock. With the possibility to create other ones like it.
• Perks, if you are good in making perks. A very good example is a perk that gives +1 AP just for moving (like Bonus Move, but with 1 AP instead of 2). It could be granted by the Doctor skill. Or some NPC could teach you to it after you do a quest for it.
Example: At your lab, you can improve yourself by leg enhancements, granting +1 AP just for moving (like half Bonus Move), requiring 135% Doctor. Works via perk.
I can not give a lot of examples, because I don't know what things can be made by perks. I have no idea if it's possible to create things like, say, bonus damage vs super mutants, or armor penetration perk. And by "perks", I mean one of the two things:
1: Powerful perks obtainable by a level-up (like Slayer, Awareness, and most of the perks), requiring a high amount of a skill.
2: Perks obtainable by some action in-game (like Gecko Skinning, Vault City Training, etc.), requiring to pass a skill check, again.
• Bonus skills! Of course, it shouldn't be like +10% at low and high levels. It should always be worth the same skill points.
Example: At 175% Speech, you can convince one of the casino bouncers to teach you Unarmed for 500$ by telling you stories of casino fights. However, the skill you gain should be based on your Unarmed skill, because at higher levels it costs more skill points to boost it. +10% Unarmed at 85% skill is not as much as +10% Unarmed at 190% skill. The bonus should be total 10 skill points, so at 114%, it should raise it to 119, not 124; at 135, it should be raised to 138 (rounded down).
• Better ammunition with bonus damage. They not be in limited number (craftable, or obtainable by constantly trading a certain item for it).
Example1: Create a simple quest that requires 175% Small Guns to start. The reward is +10 special 10mm bullets (they do double damage) + the ability to trade for more similar bullets, you get one bullet for every 20 usual (JHP or AP).
Example2: At the lab, at 175% Energy Weapons, possibility to create powered MFC, by using up 15 MFCs and 5 SECs for one. It has -40% armor modifier, -10 AC modifier, and does 5/4 damage.
Important note: I gave these ideas, because after I mentioned "unique bonuses" a few times in my suggestions for skill improvements, you asked me to give you examples of unique bonuses. These are NOT suggestions for things just to add in the game (though they can be used as such), they are suggestions to help you change the skills.
Small note: I think that after an NPC levels, it would lose its permanent bonuses, because the critter is changed, and the effects are not valid anymore. This could be fixed by a simple dialog options that grant its bonuses again.