The Muisca: Why no new religion mechanics *or* native advancement?

[Trin Tragula]

Inti is a bit of a stretch both for the Muisca and the Calchaqui though there are also some clear similarities (and the kind of challenges the evolution of the religion is set up for should to some extent fit). It's certainly true that it's far from ideal that they are now the only two tags in the Americas that don't get any kind of reforms.
Will see about making them Inti rather than animist in the future (this is an easier choice for the Calchaqui as they ended up very much a part of the general Incan/Andean cultural sphere than it is for the Muisca).

(Maybe add an option for native americans bordering inti maya or nahuta...(Does not compute... cannot spell) convert if they are animist or totemist.

Perhaps not entirely what you describe but it is currently possible to switch to the Nahuatl or Inti religions for other pagans if they capture the temples of Cholula or the Oracle of Pachacamac (Lima province).

 

[Trin Tragula]

So I decided to try out Muisca and took over the Oracle of Pachacamac and only had the option to destroy it, no option to convert to Inti. Have I misunderstood or is that a bug? Trin Tragula?

That'd be a bug, bad scope :-/ I apologize for that.

Also, while the stability cost modifier from starting as a tribal kingdom is handy for the no cb wars shouldn't they start as a tribal federation, deliberate choice or oversight? especially since my first DHE was about the rivalry between the Zipa and Zaque and the Muisca not having a true king.

That's a deliberate choice. All tribal governments in the game can be considered to have a large number of major, mid or low level power holders apart from the one you "control", the tribal federation government is for a different kind of state (as can also be seen from the bonuses it gets).

Will look into the graphics stuff