I've played Pokemon Blue on Virtual Console soon after they came out. Although I did enjoy being able to take screenshots, I'm not a fan of the grainy picture quality or the fact that you are only limited to two colour palettes(which is monochrome or this pea soup like green colour). Which can be kind of drab to look at especially considering that these are turn based rpgs. Honestly I don't understand why the Game Boy releases don't offer Super Game Boy or Game Boy Color palette. I know that it's more true to the Original Game Boy but the option would be nice.
That being said, I usually prefer playing the cartridge versions. If you playing it through any of the Game Boy line that supports colour then you get a nice choice of colour palettes. Also you can play it your TV if you have the Super Game Boy or the Game Boy Player. The image quality does seem crisper, although it might not matter much if you're playing it on the something like the Game Boy or the Game Boy Color, since they aren't blacklit.
However, the 3DS port does have some nice conveniences, such as rechargeable batteries and you don't have to worry about the battery running dry(although they are pretty easy to replace). So they do have their merits. What version you play doesn't really matter too much because by end of the day, they are the same game. Personally, I prefer playing the cartridge versions purely on looks alone.
Oh yeah, this isn't much of an issue if you're playing Yellow cause it uses the Game Boy Color's palette. The image quality still seems grainy though...