At one point in time, I would have agreed with this. I even agree with it, if it's against base Sasuke but MS Sasuke... I don't know. I give credit where credit is do, Jiraiya is definitely one of the most BA ninja in Naruto. As the OP stated, he has a large array of Katon Jutsu as well as his Gama no Kuchiyose and not to mention his Sennin Mode Jutsu.
Base Jiraiya > Base Sasuke. This should obviously be a given. Jiraiya has experience, to back up his ridiculous amount of genuine strength.
Base Jiraiya < MS Sasuke. The Mangekyo Sharingan just brings Sasuke to an entirely new level. This isn't saying that Sasuke would, "Kick the crap out of Jiraiya." It's more along the lines of, "After a long, well fought battle, Sasuke would be the victor." Between Tsukuyomi, Amaterasu and Susano, I find it unlikely that Jiraiya could beat him. Here's why; Speed. Not Sasuke's speed, but the speed of the MS. Amaterasu is said to be unavoidable, however we've seen it avoided time and time again, but that does not take away from the fact that it is, and I quote Zetsu here, "The strongest fire type Jutsu." and Susano's arrows... they also hold an ungodly speed. The only reason Kakashi lives is because he was pushed to the point of needing to use Kamui to avoid it.
Sage Mode Jiraiya = MS Sasuke. All Sage Mode is is constantly absorbing nature chakra and if happen to be able to let two old toad sit on your shoulders, your able to use a pretty neat jutsu. Now, this gen-jutsu would probably trump Sasuke if not for one, simple thing that people have seemed to over look. This is the Sharingan were talking about. "My eyes can see through gen-jutsu". Not to mention that Sasuke managed to bust out of Itachi's Tsukuyomi with his mere Sharingan, it probable that only Madara's Tsukuyomi could trap Sasuke. The only thing that could give Jiraiya an edge here is that Sasuke tends to spam, despite the strain on his body and precious eyes. Jiraiya would spend most his time trying to avoid a spammed Mangekyo technique, while trying to avoid contact with Sasuke's eyes. It would go until the other one gave out.
Sage Mode Jiraiya < EMS Sasuke. EMS... the only other character in the series to obtain this power is Uchiha Madara, and I don't need to go into that guys power. Fact of the matter is, that we've hardly gotten a look at what Sasuke's Eternal Mangekyo Sharingan is capable of besides throwing Amaterasu shuriken things. The reason that Sasuke would win here is because this totally changes my theory in the previous part, Sasuke is no longer at risk whil using these impossibly strong jutsu. He's practically invulnerable to gen-jutsu and Amatersu can burn fire. The only recourse for Jiraiya would be of course, tai-jutsu, which as I said before, Jiraiya is a bad a** dude, you never know what could happen. Susano though, it guards Sasuke. It guards Sasuke well.
Anyway, this is how I see it, if you disagree, you have every right too. If you think I'm bat sh*t crazy well... I am a die hard Sasuke fan, but I'm also fair. Ask me if I think that Sasuke could beat Madara (The true one) and you'll see that. I'm not trying to offend anyone or be one of those, "SASUKE WOULD KIC HIS ASS!" fans...