Advisor asks me to use plots that favor our approach, saying "the numbers in our paper don't matter; what matters is the message"
Standard definitions of scientific misconduct consider omission of conflicting data an instance of data falsification, see, for example, the guidelines as applied by the BMJ, or Gupta 2013 on fraud and misconduct:


  Falsifying data means altering the existing records. It is the deliberate distortion or omission of undesired data or results. 


If your advisor asks you to deliberately produce a figure that downplays undesired results, he or she is asking you to falsify your data.

So, what should you do? 

Speak again to your advisor. Tell him or her that you don't feel comfortable with the suggested plot, and explain that you feel obliged to report the data faithfully, including weaknesses of the analysis and conflicting observations.

If your advisor insists on using the falsifying plot, you should consider choosing a different advisor, because the present one may not teach you proper scientific conduct.