Some skills are useful, plenty are garbage. I cut maybe 1/3 of the skills and simplified others. Basically I'm following the example set by Hack and Slash and Papers & Pencils.
I cut PF's base skill points awarded by class in half. There are fewer skills to spend points on, so characters should have commensurately less points to spend.
Appraise: What a waste of time.
Disable Device: Have you MET me??
Disguise, Intimidate, Bluff: Rolling to avoid the fun.
Sense Motive: Look into my eye and figure it out.
Escape Artist: There is already a sleight of hand skill!
Fly: Casting the Fly spell isn't enough...?
Diplomacy: Now a passive skill called “Sociable.” I use the reaction rules from Labyrinth Lord, and the CHA modifiers listed there. You can't spend points in this except to offset CHA penalties, up to +0.
Linguistics: Doesn't teach you a brand-new language with each point. If you want to learn a new language, find somebody to teach it to you. Make a roll to understand bits & pieces of languages related to ones you know. Spend points on it as normal.
Profession: Maximum 1 point at 1st level. This is your background (villager, woodsman, carpenter, etc). Could be useful for general questions relating to that background, but maybe take knowledge or crafting skills if you want to do more useful things.
Perception: Passive skill. I'll roll it for you (do you see people sneaking up on you?). Discover things in the world by poking around and asking questions.
Spellcraft: Many magic items’ general purpose is identifiable by a character of the relevant class after 10 minutes of examination. In Epic 6 this hinges on the item's caster level - if it's above CL 6, it's beyond mortal beings, more or less an artifact. These will require research, questing, consulting sages, etc. to identify.
The other functions of the skill we can keep for now - recognising spells as they're cast, crafting magic items and the like.
-1 or less: can’t swim
0: can avoid drowning, paddle along with help
+1 or more: fine swimmer
-1 or less: climb at ¼ speed with help (friends and gear)
0: climb at ¼ speed OR climb at ½ speed with help
+1 or more: climb at ½ speed
Armour check penalties still apply. Can spend extra points to offset penalties, but no mechanical effect beyond +1.
LEAVE AS IS:
Acrobatics, Craft, Handle Animal, Heal, Perform, Ride, Sleight of Hand, Stealth, Use Magic Device: Nothing wrong with these as far as I can tell.
Knowledge: Has utility in my setting for dealing with strange monsters beyond the Barrier. Maybe you read something in an old book about this little green guy you just met?
Survival: Huge in a wilderness hexcrawl that's totally uncharted by civilization! The PCs need this to find food and water and avoid getting hopelessly lost.
FEATS: Cutting out feats altogether for a more 'old-school' feel runs counter to the entire point of Epic 6. I will be approaching this ad-hoc, and deleting feats that seem pointless or dumb case-by-case. Some 'epic feats' need to be added later if/when the PCs reach 6th level.
Item creation may get its own post, I am going to make it a more involved process: magic items should be rare and hard to find, doubly hard to make yourself. Selecting the feat is only the first of many steps.
ENCUMBRANCE: Why mess with it? You can carry one significant item per point of strength. The sum of all your miscellaneous stuff counts as one significant item (subject to eyeballing if you have lots of stuff). medium armour counts as two items, heavy armour counts as three, same goes for shields.
Example: A totally average fighter with 10 STR can wear plate mail , a tower shield , a sword , and bring a bag with some food and stuff  without being encumbered [8/10]. If he wanted to carry a lot of treasure out of the dungeon he might have to leave his shield or downgrade his armour. As it is, he should probably content himself with bringing a spare weapon or two!
This seems pretty fair to me, and reminds me a bit of Dark Souls. When your inventory system is simple enough, you can actually MAKE DECISIONS about what to bring, because the units are small enough to think about.
EXPERIENCE: Multiple ways to gain XP: exploration, treasure and defeating monsters.
COMBAT: Simplified and streamlined where possible. Attacks of Opportunity are minimised except in specific cases (a wizard getting hit while he tries to cast). This is one place I haven't dug too deep, mainly because my players don't know the rules that well. I just run combats the way I'm used to doing, and it seems to work out alright. As they gain levels and things get a bit more complex, this will require more attention.
MONSTERS: I flat-out fucking refuse to write up brand new monster stats for this game. I have shit to do. This isn't really tough since the Tome of Horrors and other books abound, except that nobody has written up Pathfinder stats for Fire on the Velvet Horizon. I have yet to reach a solution for this. I suppose I must poach and reskin stats from existing monsters as I see fit.
I'll add more to this as I come up with it or find cool links. Eventually PF will be easier to use, less annoying and make more sense, but retain the absurd variety of options that makes it so much fun.
In the meantime: