Based on the fact that there is going to be a lot of significant boss battles in e19 (Various Meteor Fights, Saphira, e4 + champion equivalent battle), and how Ame likes to be (somewhat) even with Singles vs Doubles battles, there is a decent chance that Saphira would be doubles.
There definitely are ways that a person could counter Naganadel with only Dragon types, but you must remember, as smart as Marc makes the AI, it won't be able to effectively use everything it has (which is another reason some of the leaders are much easier than others).
And no, I'm saying that if you bring something that is a counter to her strategy (not just her team) you are bound to push her over. Of course we don't actually know her strategy for sure yet, but I go back to my Hardy example. 99% of the people who complained about Hardy being too easy brought something that countered his strategy (Rock Slide Spam). They did this via a few ways (usually), outspeeding after changing the weather (typically w/ rain), changing the field in some way (which eliminated a lot of the chip damage that the field did, as well as weakening Rock Slide), or bringing steel types (who typically have high defense and resist rock, which counters Rock Slide).
In a way yes it does just come down to building a team to counter what she does. But personally I like to try to beat each leader with as few changes to my team is possible. I know that a lot of other people also play this way. But there are then also the people who bring teams designed to counter whatever a gym leader can/is meant to do and they then win easily.