Actually AQ and ISIS are pan-Islamists, as in they believe in a unified Islamic
nation, so they're nationalists in their belief in the end. AQ and ISIS also say that they're trying to kick out foreign militaries from traditionally Muslim lands, which is in itself a secular goal, because it's a fight over land, not religion. What you call flaws, I call difference of opinion. Just because you disagree with something, doesn't mean it's automatically wrong.
Think about it this way, if you change anything about yourself, because someone told you that you were different, then you'd no longer be who you are. Changing belief isn't easy, and nor should it even be considered when it comes to spirituality. Your example of Christianity is flawed, because you're only focusing on religion. How about secular movements? Communist militants, for example are just as bad; but I'll be fair here and use your Christian example. This idea that Christianity had to reform in order to stop being violent is actually completely false, it's a myth. In may cases, Christians have had to go back to their roots, not actually reform their religion, in order to stop the bloodshed. Now I'm not going to debate history with you, because that's a long and tenuous journey, so I suggest that you research about the subject yourself before making comments about it.
As for ETIM turning their fight into a "jihad" all of a sudden, I can tell you right now (just like I mentioned before) that they're using Islam as a recruiting tool, and are throwing around Islamic lingo to try and gain sympathy among the Muslim population, for domestic and foreign.
If I suddenly started using Walmart lingo to commit crime, that doesn't mean Walmart is automatically guilty, it just means that I'm using Walmart as a tool.
Robert Pape, who (specializes in political science) actually wrote a book about terrorism and suicide bombings from so called religious movements, including Al Qaeda...
Dying to Win - Wikipedia, the free encyclopedia
It's very easy to blame Islam, when you look at the conflict from the front page, but when you dig deep down to the root of the cause, you'll find that the entire situation is quite secular in nature. If Islam were to disappear today, I can guarantee you that groups like ETIM, AQ, and ISIS would NOT disappear, instead, they'd simply reorganize and use a different ideology to gain recruits.