When you find yourself trying to remember a show (or any works) that's on the tip of your tongue but just out of reach, come here - the collective brain of the TVTropes community can probably help. Post all the details you can remember (examples help). If you're looking for a trope, head over to Trope Finder. Have general questions about tropes? Visit Ask The Tropers!
Maybe Captain N?
One of the villains was Mother Brain, from Metroid, who is best described as a stretched-out fleshy blob in a jar. The hero, Captain N, was accompanied by a variety of Nintendo characters, one of which was Kid Icarus, a winged archer like Cupid.
https://www.youtube.com/watch?v=KXGr3aBln38
Wait. No. Maybe not. I just watched a bit of it on Youtube and although the entire premise of the show seems to be exactly what I'm talking about the characters and animation style don't even slightly resemble what I remember of the show. My most vivid memory of it is the fleshy villain and that's not the face I'm looking for. Also it seems like just about the last thing my brother would ever have watched. Was there some other version of the same show?
This is even less likely than Captain N, since it's more 80's than 90's. (Oh boy is it ever 80's... it's more 80's than the 80's were... wow...)
Kidd Video has a bunch of teens that go on adventures, accompanied by a flying character. In this case, it's a pixie in a leotard and leg warmers. Another mark against it is that I don't recall there being a stretched-out fleshy blob anywhere in it.

My brother used to watch a cartoon in the early - mid 90s that had a character in it that was just a flesh coloured blob living in a glass chamber. It wasn't that skinny fetus-looking four armed thing from that ocean girl show. It was just a stretched out wad of flesh in a giant jar with a face on it. Also, one of the characters was a flying boy or animal of some sort. But seriously, it wasn't that ocean girl show. I think it was kind of science fictiony. The cast was a group of young people, I think, having adventures with their little flying buddy and I don't remember if the flesh blob was the villain or some wise old fleshy dude that they consulted for adventury wisdom. Anyhow, this has been bugging me for years.