That sounds horrific, to be honest - never encountered such a bad situation.
What I used to do is giving a lot of money every turn to the Eleutheroi, so that they can actually train units in their cities and beef up against the attacks of every faction (mine included: I like to have memorable battles and not boring one-sided sieges). This usually slows down AI expansion by quite a lot, but you need to do it from the very beginning of the campaign, otherwise the Eleutheroi accumulate a huge amount of debt every turn and you won't be able to get them over it.
In case you don't know, the above is done with the console command
Code:
add_money [faction name], [desired amount, up to 40000]
So, in my case,
Code:
add_money slave, 40000
repeated at least 15 times. With the up arrow you can recall the previous command. Remember that at the start of every turn it shows something like "season summer" (or whatever is the current season), because that's the last command called by the campaign script - not the ones you called at the end of the previous turn. Internal faction names can be found in the descr_names.txt file, or in this thread.
I also tried to add money to some of the aforementioned underdogs, like Pontos or Hayasdan. Most of the time they don't know what to do with the money, though: that's AI fault, obviously. Pretty much the same as giving a monkey your credit card...
What you can do is sneakily park one spy (for vision through the fog of war) and one diplomat in key areas, and try to bribe armies belonging to superpowers. Add a huge amount of money on your treasury, take care of all your bribing and then remove the excess money to return to the original value. This is an indirect way of helping small landowners to survive for longer, and maybe counterattack. Don't expect gratitude, of course.
If you play on Medium, things are more relaxed. However, in that case you should also work your way to the world domination at a slower pace too: house rules usually help, otherwise it's plain easy to beat the helpless AI. The Koinon do start in a difficult position, but once you've secured Korinthos and successfully defended Athenai then Greece is usually in your bag, and you can slow down by a lot.
I'm sorry I couldn't reveal you any easy workaround for your issues… I hope I helped at least a bit!