I have to agree with you there. There will still be pony cons, but I'm guessing that there may be a split between those who like Gen 5, those who like Gen 4, and those who like both. I've never been to any Star Trek cons, but I'm willing to bet that Trek conventions are full of fans of the different generations. BronyCons may end up being like that as well. Whether that will be good or bad? That, only time will be able to answer--assuming that FiM actually does end with Season 9.
Though as @DarthyHooves said, once FiM does end, there will always be fanfiction to fill the gap. Not as good as seeing a canon answer, true, but it's better than nothing. Just ask any Animorphs fan.