to my knowledge the Axis allies and comintern HAVE to exist at the start of the scenario.
So you could make three small insignificant nations these members at the start.
If you look in the scenari file (1936.eug) you will see a section like this
Code:
allies = {
id = { type = 15000 id = 1 }
participant = { ENG IRQ FRA AST NZL CAN SAF NEP BHU YEM OMN }
}
axis = {
id = { type = 15000 id = 2 }
participant = { GER }
}
comintern = {
id = { type = 15000 id = 3 }
participant = { SOV MON TAN }
}
alliance = {
id = { type = 15000 id = 10 }
participant = { CHI CXB }
}
alliance = {
id = { type = 15000 id = 11 }
participant = { EST LAT }
}
alliance = {
id = { type = 15000 id = 12 }
participant = { JAP MAN }
}
the first three are the big three alliances. Here you would put the tag of the three small countries you want to head those three. The other 'alliance' entries underneath are the other alliances. You would make an entry below the last (giving it a unique id, 13 in this case) and put the tags of the Soviets and the allies (making it one alliance).
When the revolters revolt you will need to make an event that will put them into the alliance headed by the country tag first in order in the alliance wished (see the event files for who this is done).
A possible (but I havent tried it so it might not work, or work as expected) way is the leave the comintern, axis and allies alliance as is. When the revolters revolt, write an event that places them in the axis/allies or comintern and then have an event which drops the big players out of those alliances and another event that makes them create small alliances. This is of course a lot more work.
Ayeshteni