A good primer would be W.M. Watt's "The Formative Period in Islamic thought."

A huge part of the problem with understanding the historical development comes from questions like yours however, which are basically starting today and tracing history back, rather than starting with Muhammad and going forward.

To illustrate the problem let's look at the word "Sunni." The word itself is basically an abbreviation of "Ahl al-Sunna", the people of the "Sunna." A sunna, etymologically, is a well-trodden path, but it refers here to the path and example laid out by the Prophet Muhammad and his companions.

It rapidly becomes clear that the modern practical basis for such a religious practice did not exist for the first couple centuries after the rise of Islam. The six sound books of hadith that are the primary resource, after the Quran, for religious guidance did not exist. The Ulema, the religious scholarly class that interpret the Quran and the Hadith into legal rulings whose consensus forms the third source of law for modern Sunnis likewise did not exist. The doctrines surrounding analogical reasoning, the fourth source of law, likewise, did not exist.

Turning to the Shia we have a similar problem. For one thing, which branch of Shia? Looking in on Islam in 11th century one might expect the Fatimid Sevener Ismaili Shia would be dominant, whereas today it's the Twelvers.

The twelfth Shia Imam didn't die until the 9th century, so for, instance, even if we talk about the followers of Hussein, a century earlier, as being Shia, historically the shared practices with the various branching sects and succeeding groups are extremely limited and it's historically impossible to classify them as being part of a single unified movement.

For that reason, prior to the 9th and 10th century or so, there's a preference to refer to such groups as Alids (supporters of the descendants of Ali) or proto-Shia, insofar as their doctrines remained inchoate.

Returning to your question, in very broad strokes yes, there were issues surrounding succession to the prophet. But doctrinally the real distinction surrounds the legal/scholarly frameworks that accrued to Sunni Islam in contrast with a century of personal leadership by the Imams of the various Shia sects.

All of this, of course, becomes totally warped in the succeeding centuries down to the modern day, much of the discussion of which would violate the 20 year rule, but for a good overview of the kind of modern polemic we're dealing with here I'd recommend the recent BBC documentary "Broadcasting Hate" which tracks funding for sectarian broadcast networks and shows some of the level of polemic being sent out.

On your question about different religions, no, they are not, but ISIS, Al Qaeda and other groups practice what is known as Takfir, the declaring of fellow Muslims to actually be unbelievers (a person who makes such a declaration is a Takfiri.) This, itself, has a very long history, but their practice is much more closely connected to the works of more recent thinkers like Sayyid Qutb than it is, as has sometimes been made, with earlier groups that were superficially similar like the Azraq Kharajites who set themselves up as the sole arbiters of "real islam" with a mission to kill all others in the first century AH.