I give Kakashi the definitive advantage in base. He is noticeably faster than Jiraiya and far more reflexive thanks to the Sharingan's precognitive abilities. He has displayed better Taijutsu prowess as well, and has displayed proficient skill in implementing Kenjutsu (via kunai) into his CQC to the point he can match people with better weapons than him using just a pocket knife (Hidan's scythe, Zabuza's sword). Kakashi also has the elemental advantage, given his Suiton shuts down any of Jiraiya's Katons, and his Raiton affinity will grant him practical immunity to Jiraiya's notorious swamp. This is not to mention Kakashi's Genjutsu prowess, which forced Gai to develop an entire fighting style just to cope with it, and also allowed him to match the likes of Obito in an illusory struggle.
When it comes to a battle of trump cards, Kamui is far more accessible and dependable than Sage Mode. It can be activated on the fly as opposed to Sage Mode, and is practically undodgeable unless you're a Hiraishin user, or BM Naruto. Assuming Jiraiya gets into Sage Mode, he lacks the speed to dodge Kamui and will ultimately get warped. No chance of Kakashi missing either when he nailed BM Naruto who was moving fast enough to be dodging Kamui propelled stakes in a chaotic environment that had tons of debris and rocks flying all over the place. Jiraiya has neither the speed nor reflex feats to even become a candidate for dodging any Mangekyo technique, let alone Kamui.
Overall, Kakashi's base form > Jiraiya's base form. Sage Mode Jiraiya > Kakashi's base form. However, Kamui allows Kakashi to shut Jiraiya down whenever he wants.