Yeah, it is a tough choice, but I am gonna lean towards Paul, and I'll tell you why. As much as people hate Paul and his training methods, it got him all the way to the Final 8 of the Sinnoh League which was a huge accomplishment. Sure, he looked like a weakling next to Cynthia but I mean come on she's the champion. And he didn't do well at all against Brandon (again, a very strong trainer). There's not much to base this on though since we really haven't seen Paul and Gary in action at all really except against Ash.
I agree with Bullkid. Gary is now a researcher so he is obviously spending less time training now and it showed when he was defeated by Commander Saturn and Hunter J and her grunts. Blastoise used to be a powerhouse and the fact that he went down so easily against either Hunter J or Saturn (I forget) is really telling. I know Galactic and Hunter J train their Pokemon but probably not to the extent that a Pokemon trainer would.
Gary is all talk when it comes to Pokemon battling I think. He is good don't get me wrong, but in the Indigo League, he was out rather early and in Johto, he did do better but not as good as Paul did in Sinnoh. We don't know how Paul was as a trainer in the beginning so we can't really judge. Gary had some impressive one on one wins against Ash, but Paul's first six on six battle really showed how strong Paul could be.
Like I said, we can't judge too much since we didn't see Gary battle that much, but I will say Paul. Paul is still training hard as we speak.