Skills have been my special hell for 3E and PF1 for years. As far as I'm concerned, 3E's designers can eat a bag of dicks, and Paizo can have the leftovers. Huge list of skills; never, ever enough skill ranks unless you run something like a rogue or PF1's investigator.
I appreciate what 3.5 was tryng to do, which was provide a mechanism to model a wide range of character types and to allow genre-specific/world-specific customizations. The major stumlbing block is its virtually impossible to balance, made worse by the 3.5 trying to set static DCs for actions that don't properly take into account counter actions; things that 3.5 treats linearly should be exponential/logarithmic.
My ideal sytem would be some sort of heirarchy. Points you spend in general categories enhance specific skills, ranks in specific skills give greater advantage than generalities. I would also add that skills shouldn't just be INT based and shouldn't be granted at level up, it should be granted for downtime actions or quest actions but that's going to far into the weeds.
If only 4e was developed a bit more in the skill/ downtime field…
4e's decision I can respect just from a "shut up and play" perspective, adn that 4e is more about fantasy super heroes than Tolkienian ones.
Skill challenges/ritual casting DCs provide better depth than people give them credit for. The issue is they are an extreme overcorrection from 3.5's "hope you realize you've stumbled into an important situation and get the plot point you supposed to get!".
I used to hate skill challenges until I read a blog about Call of Cthulhu and that mysteries/investigations should not be to see if the players succeed or fail; they should always succeed. The investigation should be about determining the level of success and the cost of that success, and when you view Skill Challenges through that lens they become much more useful.
I have
opinions on this especially since it is very anti-B/X, but I feel the expected GM mentality 3.5 material puts forward is too much "hope you got the right combo of skills and rolls, fucknuts!".
(To expand a little more but not too much: B/X adventures tend to be written with multiple ways for the party to be drawn along the adventure regardless of their actions - missing a key item only makes things more difficult on the party, and encourages re-investigation should it be needed. If you don't bring the French Tickler of the Grand Abbotess with you to fight the lich, either you can't open the door to the phylactery and the party sees multiple hints about what they are missing, or you fight the lich being unable to counter his Bad Touch.
3.5 adventures seem to be written for "The party discovers the name of the shadowy figure running the criminal enterprise at the docks by interrogating the theif they caught on a 12+ intimidate check. It is also written on the wall of the orphanage's outhouse" but the adventure being written such the party needs to find out who they are looking for without much consideration given for "What if the party fucks up their roll and also misses your clever hints to take a massive shit when visiting the orphans, or just doesn't visit the orphanage?"
edit: Or if the party discovers some information before they would otherwise do so via lucky roll, unexpected use of magic/magical item, suddenly the adventure is fast forwarded but potentially without the party having the needed other bits. Spells like Talk to Dead make murder mysteries trivial to solve.)