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If Jacen didn't turn to the dark side and the GA remained intact without the Second Galactic Civil war and the the Tribe invaded, who would emerge victorious? A Jedi Order that is just rebuilding itself after the Yuuzhan Vong war or the Tribe?

The New Jedi Order has superior Force users (Luke, Kyp, Kyle, according to the OP a light side Jacen, etc.) and technology (Stealth X's). Also, if Daala isn't in charge since according to the OP this was if the Second Galactic Civil War didn't happen the GA would support the Jedi.

NJO. No way would the Skywalkers and co. be allowed to lose.