I know all three had separate regional interests and political divisions, but only the US held together despite a civil war. Was it just because in the American Civil War the two sides were so unequal? Could the South American states have held together somehow?
If someone knows more about the First Mexican Empire or the Federal Republic of Central America, feel free to contribute.
With Peru-Bolivia, I assume you mean the Peru-Bolivian Confederation right?
A major reason would be how profoundly the economies in South America were damaged during the independence wars.
The American Revolution lasted less than a decade and didn't result in the overthrow of slavery or other key economic structures (at least for the most part).
Gran Colombia's respective independence wars started around 1808 and went on for almost 20 years. During this time slave plantations were almost all destroyed an abandoned. Mines (more important in Peru-Bolivia's economies, we're abandoned, flooded, and collapsed. Independence went beyond a political war led and organized by white elites to become a somewhat broader (though still mostly white) rebellion against various injustices of the existing order.
It was American Revolution and American Civil War wrapped into one.
By the mid-1820s Hispanic America had been economically devastated and now faced the issue of paying huge loans at hefty interest fees to British creditors. All while keeping themselves on a war footing because Fernando VII was sending late expeditions to reconquer Mexico as late as 1829!
On top of all this, Hispanic America didn't get together and jointly agree on how and what independence should look like. Colombia contained modern day Colombia, Venezuela, Ecuador (etc.) because Bolivar happened to be the one to free them. There was no formal act of submission or suffrage by locals that gave Bolivar the mandate that Washington had.
Sorry I can't speak to the case of Peru-Bolivia. Been a while since I read up on it.