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Gym leaders, elite 4 and champion have a fixed number of pokemon for use in battle of 4,5,6 each with the exception of brock mist that carries 3. Only their main pokemon is fixed and stays in backgroud alongside the leader while isnt its time to battle (like your pikachu/eevee) and are always sent out last, their other pokemon are random sets of a pre fixed list for each leader (like battle tree)
Trainer pokemon has a better ai, also each trainer type equips a kind of item in all mons (ex: bug cathers has all pokemon equiped with silver powder)
xp gain continues flexible
you have an opition in the ball throw menu to sent out one of your mons in wild battles, pokeball throw however is the default menu.
each area has a "boss mon" which is a mon of that area but superior in strengh also can be an evolved form, to catch it you must battle it first and defeat it. They appear randomly but can be summoned by placing berries in certain spots. After become champion, boss mons have an updated list, come in highter level (50-60) and have higher chances of being shiny, legendaries that were defeated or caught can respawn as boss mons again but rarely. In a hipotetic world were this game doesnt have 151 only, national dex mons appear as boss mons post game
co-op are now 2 vs 2, and trainers with only one pokemon use a copy of their first pokemon
too hard? Pokemon refresh is anything you need, pet your mons a bit and they gains the same boosts of always
still hard? New function called "friend assist" You can call your "friendly rival" that will battle ai controled alongside you using mons a bit stronger of the oponent mons. Gym leaders and important trainers however will also call an assistant, not strong as themselves. Co-op work as a friendly assist.
the champion battle is against friendly rival (who has matured and became more confident). If you use the the friend assist it will call Red while friendly rival will call Blue and last battle is a multi battle