Best option for MMO game? I don't understand some things.

Bluntly the truth is, using PUN is simply not an option unless and I say this in all seriousness, unless you can make each piece of the map a separate room (E.G. - the regions)... Like example lets use Guild Wars 2 as an example.

Yo are in Ascalon City, well - force a set number of players E.G. 5 players max per room, after that - it creates another (room) for 5 more people to join that same room. Then have it when you walk outside the city (or ANY) transition between loading levels/regions to be a room with a limited number of players.

So steps

• Load game
  
• Join or create a server based on where you want to go
  
• if there is an available room for that (specific level) available - then join it.
  
• if the room is full - create a new room for that level and allow others to join it
  
• if you try to transition into another *(loaded) level area, do the same steps as above.
  

But you will NOT, under any circumstance with PUN be able to handle E.G> 60 people in one area.
Now with Photon Server, you are free to design how you want, using multiple servers and blending them, etc. Won't be easy, but hey - if this game is something you really want to make, then getting the server licenses and gaining the knowledge to do just that won't be too much for you.