First is probably an unpopular opinion, but I actually really like Iris. I did already discuss her in my recent blog, but while she doesn't do much at all throughout the story, I mostly liked her for two things: one, her battle setup with the full body art in the VS animation, that epic rainbow beamed battle scene, and let's not forget that battle music that I NEVER get tired of hearing. Two, the fact that she uses many of my favorite Pokémon, including my favorite of all time. While she's not overly hard, i've still always found battling her to be very fun, especially on Challenge Mode with her 100-120 power STAB moves *cough Outrage Haxorus cough*. I remember the first time I battled her in the rematch, that Salamence caught me off-guard big time. All that aside, as I mentioned I also found her a pretty creative choice as Champion, and likely not someone that a natural player would probably expect. So yeah, those are things I enjoy battling her for.
For that matter, I do like Alder, as well, mostly for the fact that he actually steps up to try to fight the main villain. Not only that, but he has a story to him in the sense that his Pokémon died.
Last, but probably not least, is Cynthia. Her personality throughout the story was cool, although as I mentioned in the 4th gen forum I don't like how she does nothing against Team Galactic. But then we get to battling her at the league, where we all know her for that Garchomp, as well as Spiritomb and her other vicious threats. She almost always makes for a fun battle given the strategy you usually need to come up with against her. And I like how she returns in the Unova games and you got to battle her there.
So personally, as far as battling goes i'd go with Iris, but overall i'd say Cynthia.