Here are some stuff I'd find helpful as a beginner. I hope it helps.
How do I combine x and y?
Menu - PokéGear - Crafting Kit
IV Candies, where?
Roarin Island, west.
How do I evolve x?
If normally evolves through trade, it evolves at a specific level. Stone evolution is the same. If evolves through trade+held item, just make the Pokémon hold the item, level up.
How do I find x Pokémon?
Check the location guide, first post of the thread. If not there, then it's either an event Pokémon, or it simply doesn't exist yet.
How do I beat W.T./Rayquomi/a wild Rattata? How do I get stronger?
Max IV/EVs (Roarin Candies/Training Safari), find cards of your Pokémon (Asutra City), find shiny/plat Pokémon (Auction House). Grind.
How do I find this item?
First post of the thread, check item guide.
I did this thing, what do I do next?
Check the thread, check Google, if nothing turns up, ask here. After getting Rocket Wings navigating will be easier.
GP, how?
First post, custom mechanics guide.
Shiny rate?
1/256, no way of increasing afaik.
Where to grind?
Depends on your level. Most cities have Blissey/Chansey/Audino farmers. Beyond lvl 100, Deshret, follow the Talonflame road, go north, beside the crossroads there is a guy with lvl 90/100 Mech Blisseys. After being done with Deshret quest, go back in time, there's a guy with a lvl 150 Mech Blissey team. Costs a buttload of cash.
I absolutely loathe puzzles, gimme answers!
People who solved them the hard way will be reluctant to just hand you solutions. That being said, there are plenty answered here, also check Google/Youtube. If still nothing turns up, obviously nobody bothered to type it down. This is not an official game, some things will stay obscure unless Stoc himself makes a walkthrough.
How do I (casual stuff)?
As I said, this is a non-profit, community game, answers need to be given by people. Large fanbase means more answers, small means less. If people didn't type in something specific, then the answer simply doesn't exist yet. For example, let's say you'd like to know where to get more Ether. If nobody's interested, or it's just a minor thing, then it'll stay unanswered, despite having a fairly easy answer. (Afaik nobody sells Ether, but you can mine them in Krystolny)
How do I (something obvious)?
Guides. There are guides. They exist. If you don't believe me, check the very first post of this thread. You can even use Ctrl + F to search within them. Technology. Wow.
Tips:
Said it before, if you compare a 5 GP, Platinum Shiny, Max IV/EV, Plat card attached Pokémon with a regular one at the same level, your mind will implode. Try to do at least some of these.
Build a decent team. Empyrean may not be a grindfest, but it's also not an "all Pokémon viable" game. You may adore Sunflora, but it will be absolutely garbage. If you're not sure, try pokemondb.
Check rocks, odd looking tiles, out of place objects. They sometimes contain loot. Sometimes actually important loot.
There are some stuff you can't get to early in the game, come back after getting Boat/Boat Upgrade and Rocket Wings.
Houses. Buy them. Rent them. Things are expensive.
Also mentioned in game, if you plant Amida Apriplums in all 5 possible places, harvest and sell them, it'll net you decent money every 3000 steps walked. Forever. Combined with house rents you'll bathe in cash.
Auction House. Sylen City. Requires 1000 steps and 24 hours to reset. Don't abuse it if you value having fun.