Lately I've taken to MountainCoast. It's been much less likely to cause a MAF than erebuscontinents or worldoferebus for me, although I do wish that selecting "continents" over "pangea" seemed to do something. At the same time, since I normally play RifE, multiple continents would probably just get absurdly barb infested, even though I play with No Lairs anymore. As far as size, I usually play standard or large--nothing over that, because even large tends to rack up mafs really easily mid to late game. I play with randoms, but I tend to use RifE's restrict random civs option to prevent several. Most notably, the lizardmen civs, which I find overpowered with their auto climateform to nasty jungles, the chislev which I find flavorless, and a few others which just don't do much for me in terms of flavor.
On the whole, I think balance is in how you handle things. For example, two recent games started with all civs annoyed at me. One of them, I was playing Risen Emperor and I never did anything to really make friends, counting on a strong military and culture to keep me safe, but I ended up instead having pretty much everyone attack me.
On the other hand, the other game was as Flauros, and as I went along I took care to create a bloc of allies using the undercouncil, tech trades, and strong military/expansion/selectively building people's favirite wonders. This time I was able to create a strong front of allies, at the expense of making a more solid bloc of enemies too. But when I finally did get dogpiled (I had finally acted to attack someone, since no one had dared attack me, but they peacevassaled to Sabathiel/Basium, and then Thessa who hated me joined in) I had allies to bring against them, and strong enough military that I suffered no significant losses.
So, while it's possible to have unbalanced setups, I ultimately think that the balance between sides in a given game is what you make of it, and there aren't really any situations where it's impossible to create a somewhat balanced set of alliances through play, even if doing so may at times be difficult.