I've already suggested this idea numerous times. But this version of the idea is ludicrous and too much.
1 ) For a PokeRaid to even be considered "possible", you have to look at what game mechanics have already been done at the most; 3 Vs. 3 Battles are the biggest battle you can have in the games.
2 ) You would need to address a "Party System". But the maximum being only 3 Trainers in a Party.
3 ) Most MMOs also allow for individual Party members to run off and explore/battle on their own with the option of a friend suddenly coming up to help them finish them off. You can't do that in PokeMMO. Which would make it difficult to get around. The only way you could do so is every Battle before the PokeRaid's Final Encounter are for Trainers to individually battle by themselves. Primarily Wild Pokemon Battles (with uncatchable Pokemon). End of certain paths would end in 3 Vs. 3 Battles to advance further into the PokeRaid.
4 ) The Final Encounter itself, while logical to have it just be a single, very powerful Pokemon that has been augmented somehow, would probably have to be a variation of: 1 Single Over-Powered Pokemon & 2 Smaller Minions. Or 3 Evenly Powerful Pokemon. To have 3 Trainers battle just a single Pokemon would take away from the already established 3 Vs. 3 mechanic and would make coding a Hell of a lot easier.
5 ) Pertaining to the "what happens if someone leaves mid-Battle" problem. Instead of a cooldown system where it skips their turn, why not just have a randomization occur after 20 seconds where the game would choose 1 of that Trainer's Pokemon's moves at random to use?
6 ) How many Pokemon could a single Trainer bring with them? Logically, a single Trainer's team is 6 Pokemon maximum. In a battle, that's all you can carry. 3 Trainers in this sense would be 18 Pokemon which would be overwhelming. Instead, before each PokeRaid, have a PC beside the NPC that allows you to enter the instance where you can deposit 4 of your Pokemon, bringing only 2 with you.
3 Trainers x 2 Pokemon each = 6 Pokemon total. This way if one of your Pokemon faints, you can still have a back-up and not feel completely useless.
7 ) As for "Loot". Instead of giving some kind of PokeMMO-exclusive item or something overly powerful. And this is going to sound potentially impossible... Why not find a way to code in a whole new area in your Item Bag for "Avatar" and allow people to earn all 5 available colors for their Avatar (Red, Blue, Green, Cyan, Black)? But possibly piece by piece? Hat, shirt, shoes? You could have various combinations of colors on Players running around endgame which would make each Player look a little bit more different than everyone else.
Added fun? Have spriters create whole new color schemes for special times of the year like Christmas/Halloween/Easter/Summer/Winter/New Years/etc. that you can earn too?