I found it to be a wash. I filter all of my reconstituted peptides, so the extra waste is negligible if at all. Instead of filtering into a sterile vial, it goes into the pen cartridge. The pen needles create somewhat less waste than insulin syringes.
Aside from the original pen cost, I’m finding 3ml cartridges to be cheaper than 3ml vials and pen needles to be cheaper than insulin syringes.
In the end, there’s not too much of an advantage or disadvantage to either set up other than personal preference and maybe ease of use. My preference is the pen.