Her Haxorus is at around level 60 (if I remember correctly).
You need to train the rest of your team more, so they can deal with the rest of her team, meaing that your Emboar can be used last in the battle, and use a STAB fighting move to deal with Haxorus (maybe something like Superpower, but be careful since her Haxorus has Focus Sash). The Move Tutor in Lentimas Town will tutor Superpower for 10 Blue Shards.
Your Emboar should be able to deal with Hydregion with one STAB fighting move, even something like Brick Break should be able to finish it off. Also give your Emboar Leftovers, since it seems to be your main Pokemon (also just remembered that Brick Break is a TM only obtainable via PWT, so just stick with Superpower).
I was going to suggest giving your Keldeo Ice Beam, but I just remembered that it can't learn it. :x
Personally, I ended with my Samurott using Ice Beam, but I don't think there are many water Pokemon around at this stage.
You can catch Marill at level 35-50 at Victory Road in the cave by surfing, or you can go back to Humilau to catch a Jellicent at around level 40, but to be honest, I would just train your team further and use your Emboar to deal with Haxorus.
I also would not use your Flygon for this battle unless its level is significantly higher, because Iris' Hydregion and Haxorus are fast and will KO you before you can deal damage.
Most things in game can be surpassed with relative ease if your level is high enough.