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The actual 3ds doesn't have too many noticeable frame drops but when I see it on the monitor, it gets more choppy. Not unplayable, just not as great as I'd prefer

There's a decent chance this is just psychological. Lower framerates, stuttering and input latency are generally less noticeable on smaller screens because the screen makes up a lot less of your overall field of view.

I'm seeing this too. I'm playing Bravely Second, and it gets choppy every few seconds, where it's constantly smooth on the 3DS screen.

Unplug other devices from USB and see if it persists. Chances are something is hogging up the BUS.