Curiously, I've been developing a setting based on the premise that lizardmen and yuan-ti are the main antagonists of the entire setting, so I'm on the same page with a lot of folks here. The entire theme of that setting was vs. the reptiles. I gave them a culture a bit more like lizardmen from Warhammer, but that mostly means high level mages, and dinosaur-riding villains, which allows for them to last as useful antagonists at practically any level I would seriously consider playing. The yuan-ti were more sneaky. And the yuan-ti and lizardmen were the big rivals for power on the continent, while the demihuman communities lingered in the shadows. Maybe subconsciously, I was mimicking the view of mammals of the Mesozoic, living in the shadow of the dinosaurs or something.
I also have, as rivals but possible allies to the deminhuman communities, a Planet of the Apes style civilization lurking in the corners of the setting somewhere too.
Here's a couple of posts from my blog, in case you're interested... although this is probably much more dramatic of a shake-up of basic D&D tropes and conventions than you're looking for.
http://darkheritage.blogspot.com/2013/10/odd-d-part-vi-lizardmen-kingdoms.html
http://darkheritage.blogspot.com/2013/10/oddd-part-vii-yuan-ti-kingdoms.html
cool idea - I ran a side adventure years back with a similar idea - Lizard Folk based on Warhammer Lizardmen. XP awarded.
In mine, the lizardmen ruled with the equivalent of the Slann Mage-Priest as almost near demigods on the world, and humans and halflings were kept as slaves, or else lived out in the dangers of the wild, while yuan-ti were harsh and somewhat rebellious "captains" who served as leaders of the lizard armies. (I have a Slann Mage-Priest mini, so wanted to actually use it in a D&D game...)