I was listening to the Roll for Initiative Podcast, and they were talking about non-weapons proficiencies and "skills" and it dawned on me when skills work and when they don't.
In BRP you have skills, lots of them. You also have stats, and sometimes you roll against those. Usually those are the Luck, Know and Idea rolls which are stat x 5 for a percentage. More often than not, those are only used when there are no special skill, or for specific procedures or mechanics detailed in the rules. The specific skills are mostly based on the development points you put in there, even if high stats might give you a slight bonus in some incarnations of the system, like my beloved Stormbringer.
In Warhammer (1st and 2nd ed. at least) you mostly roll against your stats (weapon skill is a stat, I'm just saying...) and the skills you have just gives you a bonus to a stat check. They are mostly feats or talents to diversify your class. You either have a skill or you don't, so you don't develop them with points.
In 1st ed. AD&D (and 2nd ed.) the proficiencies are legion, and they are bascially skills for lot of different special knowledges. To use them, you basically roll a stat check, with a bonus.
In the Nalfeshnee edition (Type IV you know?), you have a very short list of skills. They are based on development points, but bonus from stats play a significant part. You roll the same die as when you, say, make a save.
Do you see some patterns?
This is how I rate those system on a subjective enjoyment level.
1. BRP skills are fun, worth my time and they make the game interesting
2. WH skills are nice for colour, but I depend on my WS and my I.
3. Why not just roll a stat check?
4. "I need to solve this problem? Gee, I wonder what I will choose? I seem to have one skill for stealthy stuff so I roll that I guess. Was it just like a stat check/save you said? Can't I just use my DEX?"
While it might not be the same thing for everyone, I think I've found out what works for me. In 4th ed. they don't really present you with much a choice. You can have any colour, as long as it's black. right? In WH I have a schtick which I can groove on for colour. Nice. In AD&D, why didn't I just roll my DEX?
I think a game which uses skills should have a mechanic that feel fun and involved and don't feels like it could have been a stat check. They have to be something clearly different from a stat check. Preferably they should be something which not everyone off the street can be expected to have access to. Also, when you have a cool skill mechanic, the choice to roll a specific skill must involve some choice and diversity, to allow for multiple ways to place those development points while still build viable adventurers.
Your mileage might differ. I really like CoC, RQ and Stormbringer while 4th ed. bores me to tears. My summary would be: if you tack on a skill system, make it large enough to matter and roll off your stats otherwise.