-Earthbound vs Undertale (Ik Original vs Inspired MUs are boring, and UnderBound MUs are certainly guily of this with the notable example of Frisk vs Ness, but I think this is the exception)

-Overall tragic main antagonists (at least after Giygas' defeat) from RPG games who at first were just kids but after some timeline shenanigans (With Pokey traveling through time and Flowey messing around with the timelines and his overall SAVE/LOAD abilities) became corrupted, sadistic, cruel and powerful megalomaniacs who sought out the destruction of life itself.

-Even before their time shenanigans messing them up really bad, the breeding ground for their corruption was because of something they basically didn't have control of (Pokey's abusive parents and the Mani Mani statue, and Flowey feeling no emotions due to lacking a soul and therefore lacking empathy ig?).

-Both didn't seem to have a major part in their story, even with them popping up once in a while to toy around or taunt the main protagonist (Pokey first just seemed like a fairly innocent kid who acccompanied Ness, but later he became a major antagonist with him helping out Giygas until eventually becoming the main antagonist of Mother 3 and Flowey just seemed like a random asshole before revealing himself to be the game's main antagonist).

-Both have had a friend, being a kid with a striped shirt, which they eventually lost (both figuratively and literally) and seemingly still can't get over them even after they're long gone (Ness and Chara). It's especially weird since now it doesn't really seem like they like them (Pokey seemed to despise Ness in Earthbound and Flowey admits Chara isn't really a good person).

-Both became powerful and nigh-unkillable beings after a certain point in their story, becoming one of the final threats (Pokey becoming an immortal manchild after time traveling so much and Flowey, after obtaining the Human SOULs, became an all-powerful god).

-Both manipulated the brother of one of the more major characters of their game to achieve their goals (Pokey transformed Claus, now known as the Masked Man, to help him pull the Seven Needles so that the world would be destroyed and Flowey manipulated Papyrus by getting on his good side and used him to gather up the Undertale cast so that he became a god).

-Both were also in some way abused or bullied by someone in their family (Pokey being abused by his parents and Asriel, prior to becoming Flowey, presumably was bullied and psychologically abused by Chara).

-Truth be told, however, they're honestly just kids who became evil due to their rough upbringing and despite their evil tendencies you can't help but feel bad for them in a way.

Not really connections as much as they are cool tidbits, buuuut:

-They both have been compared to each other in official Earthbound material

-Flowey possibly references one of Pokey's line

Connections so far, there might be stuff I missed so once I find more I'll be sure to update them.