1, Hotkey option where you can put any item (like ocarinas, bike, leppa berries, etc) / or any outside battle effect move (like Sweet Scent, Teleport, Dig, etc).
2. There will be color difference, it will say Shiny in name, and shiny effect animation goes off in the start of battle when a shiny is encountered.
3. Any wild encounter there is always a 1/30k per encounter chance that a shiny will pop up. Egg hatches have the same chance of finding shiny as well. If you use a Donator Status, it improves the encounter chance by 10% to 1/27k.
4. You can farm items like amulet coins, etc which are always in high demand. Farm breeders (31 IVs, etc)... or best bet is dittos, they always sell, even bad IV ones (cause people who are egg hatching in hope of shiny need a steady supply of dittos). Can do payday pickup (preferably with a level 100 Meowth), Vanity item trading, GTL sniping etc etc lots of ways. Do whatever suits your playstyle and time availability.
5. There is trainer pickup which lets you pick up basic stuff like pokeball etc when you finish a wild encounter. However this chance is not quite high and the items are not that great / expensive. However if you are leading with a Pickup ability pokemon, you can pick up the best items there are to acquire in a certain area. For example, Leftovers in Berry forest, Shards in Undella Bay, etc etc. Refer to the pickup guides in Guide Tavern for more info.
6. Yes you can re-battle trainers. And once you finish a region's storyline you can rebattle the Gym leaders in it as well. Gym rebattle run is one of the most common pokeyen earning method for many players (hence why the high demand of Amulet Coins)
7. Yes every region has a breeder. However breeding works differently here, you lose both the parents to get one egg. For more information refer to the breeding guide in Guide Tavern.
8. You can win official PvP / PvE events and be rewarded some RPs (reward points), or you can farm pokeyen and use it to buy RP vouchers from GTL / trading via other players. Apart from this no other way to get them than to pay real money.