Well in the term of raids it would really not be that hard to make the real problem would be the ballancing.
Since you could easily use the concept of double battles in pokemon and then instead of just two people make it 5-6 people and bam you have 6v1 boss battles but how would you balance it? For starters you would need to have custom made boss mobs that have health grater then the equal of the average of 6 units and probably even more at that.
Damage wise it could be no better then it currently is in game.
Healing wise would it be potions or would you make it so trainers would have to dedicate 1-2 members of the group to having pokemon that can use healing skills.
Tank well i don't think this would be an option since for it all to work relativity well you would want the boss to hit more then one pokemon at a time otherwise it would just get static.
All in all i don't think the idea of raids is a good idea :D
Factions on the other hand, It could work Once players have beaten both E4's give them a option to join "Red" or "Blue" by joining one you are setting your self in stone.
There could be daily quests with rewards such as "Capture 5 pikachus for the grater cause" You would hand in the 5 and get a reward depending on what the gm's found to be suitable.
There could be also inter faction pvp where the top faction at the end of the season (a month? or more?) could gain access to custom made area that has pokemon a bit higher in level then the cerulean cave? for leveling purposes.
Although if this was added it would also have to be made so 1 faction could not be more then 2-3% bigger then the other.
I don't really know just some ideas.