Honestly, I don't see Team Flare interrupting the Alain/Ash throw down in any way.
Likewise, I am 95% positive Ash will beat Alain in a fair, uninterrupted fight.
At this point, we just need to think about it from the writers perspectives: they want the highest possible ratings, and viewer satisfaction so they can keep everyone hooked for the next season. With that being said, their goal would be to ultimately hype the final round up as much as possible, and to NOT piss everyone off so they stop watching.
So, I want to safely conclude that the following infuriating scenarios most likely won't happen (in order from most to least infuriating):
-Ash-Greninja is about to get the knockout win on Zard X and win, but Team Flare interrupts (seriously, imagine the backlash if that happened!)
-Ash collapses from exhaustion from Ash-Greninja phase during the fight and Alain ultimately wins. Later, during Flare confrontation, Ash gets his "retribution match" and "wins" (this may be worse than the first one; it wouldn't be revenge, it would be rubbing salt on a festering wound)
-Alain wins in a straight up uninterrupted fight. I personally don't think Alain will win the league; to me it makes ABSOLUELY ZERO SENSE from both a plot and marketing standpoint. First off, as others have already stated, Alain would get zero development by winning, this inflating his already big ego that he is the "strongest mega evolution trainer alive" and that he is "able to protect the person he loves" (or whatever it is). Furthermore, from the marketing standpoint, Ash will have a grand total of TWO FULL LEAUGE BATTLES! People are already mad about that, and it makes no sense for that to be the case, UNLESS THEY HAVE MORE BATTLES PLANNED AFTER THE LEAUGE! But what battles you ask? Well, IF ASH WON the Kalos leauge, it's highly possible he would challenge the Elite Four/Diantha, thus devoting more episodes to the leauge, which would make sense.
So, case in point after my long rant, I think Ash will win the Kalos Leauge in a fair uninterrupted battle, and would most likely fight for/become the Champion. After that, I'm not sure. I would guess he would have to stay in Kalos to defend his title (believe Diantha once said that was required at some point) so I could see a totally new main character for Su/Mo anime.
Anyways, if you followed me this far, what do you all think about my theory? It's just me recording my rambling thoughts on this.