Kaidan comments in ME1 that his L2s allow him to spike higher than most L3s in combat, with a Biotic Shepard being a rare exception.
I guess he could have been lying about the last part to downplay his abilities and not show up his new boss, which does seem in-character for him. But if he was telling the truth and Shepard has more biotic potential and power, I still think Kaidan might be slightly stronger (at least in practice), due to him having far more experience and training from BAaT when it comes to using his abilities.
The background for a Biotic Shepard is that they were one of the kids who manifested as a result of secondary exposure to Eezo, between the time when BAat was shut down and Grissom opened several years later. Shepard was only identified as biotic after joining the Alliance, where they were fitted with implants and given a crash course in how to use biotics alongside their basic training.
Not to say the Alliance would send their biotics away with an afternoon course under their belt, a handbook and a simple "good luck", but I doubt the Biotic course that they put them through is anywhere near as gruelling as BAaT or intensive as Grissom later on.
Then again... Shepard has had about a decade or so to catch up on their own, so it probably evens itself out in the end?