>>56941907gonna go out on a limb and say phione. even when manaphy is obtainable (like in BDSP) you have to actively look at your manaphy and go "yeah i want a worse version of this" and then take the time to breed it, hatch it, and grind it up to get it on par with the rest of your team.
random NFEs get used just because people like the design or they caught it and never bothered to switch it out because they're doing the overleveled starter thing, but i can't imagine people actually ever used phione for any reason.