@aspiringgirl, that usually doesn’t matter, as the usual math sequence is:
Pre-AP Algebra I --> Pre-AP Geometry --> Pre-AP Algebra II --> Pre-AP Precalculus --> AP Calculus AB or BC, depending on which one you decide.
Since you were 2 years ahead in math entering high school (having completed and received credit for Algebra I and Geometry in middle school), naturally you finish the math sequence earlier by the end of your junior year. Those who are 1 year ahead in math would finish the entire sequence by the end of their senior year. It’s well known that the endpoint math at most high schools is the AP Calculus BC course. So it wouldn’t look any “better” per se on an application, as Calc 3 isn’t a usual offering at most high schools (or it’s part of the AP Calculus BC course), or at the very least, it wouldn’t look “bad”.
There’s always AP Statistics as well.