Best/Easiest way to transfer Pokemon between emulated FR/LG up to US/UM?

[MultipedBeatle]

I recently began a playthrough of the Pokemon games starting with FireRed and LeafGreen with FR/LG+, and was wondering about transferring my Pokemon up through the generations. I have looked up the topic and many suggested using PKHeX to edit the save files to bring the Pokemon into my PC or party, but I want to bypass anything like that as long as I can. I know that you could plug the cartridge into the bottom of the DS Lite to transfer the GBA Pokemon, however I am using a 3DS with an emulated copy for FR/LG on my PC and my copy of HG/SS downloaded for use with the Twilight Menu. What would be the best way to transfer these Pokemon through the generations in the most "vanilla" way possible? I have two 3DS consoles, with one that I could also homebrew if I need use IR or wireless to trade, so that is on the table for me. Thank you so much!