Virtual Console. I grew up with a gameboy color and experienced red, blue, yellow, gold, silver and crystal that way, so I do get nostalgic thinking back on it. I had a clear limited edition gameboy color that you could see the insides of-- t'was beautiful. The old cartridges were also nice to look at, such thick plastic with bold colors that you don't get to have and hold on an emulator or the virtual console. There were also some nice features you could utilize if you had a gameboy that you can't make use of now without that like the gameboy printer to print out diplomas, messages + other cute pokemon pictures and Dex entries. I also have memories of taking my pokemon from the gameboy and loading them onto pokemon stadium for tournaments with the transfer pack.
That being said though, I still have to choose the virtual console because it allows me to transfer the pokemon I go on adventures with in gen 1 and gen 2 games over to more recent generations, and continue raising those pokemon in other regions. Whereas on the gameboy there is no way to trade beyond gens 1 and 2, so what happens in those games has to always stay in those games, unlike GBA games that can allow you to move your gen 3 pokemon over to gen 4 if you want, and then onto gen 5, 6, 7, 8 etc.
Also the batteries in the Gameboy cartridges will have run out because of their age, and with the old Gameboy games you can't hold a save on your progress unless you replace the battery, so not being able to move through the region at your leisure would bother me. Even though this can be fixed, playing the virtual console on your 3ds is simpler and cheaper to do than the labor of love of trying to repair an old game, at least to me.
The Virtual Console comes with some other perks like the gs ball event being added to the international virtual console releases for Crystal. Getting my first Celebi at the end of my Johto journey was pretty awesome. It's also neat that pokemon from the virtual console always have their hidden abilities when transferred out.