I don't feel very strongly about bosses in Sonic games, I agree. The final bosses usually make for good set pieces, but they're not that hard. I was obsessed with Finalhazard in SA2 as a kid though, I think the space setting + Super Sonic + Live & Learn etched a permanent mark on my childhood mind.
I will say though, I think bosses in platformers are usually mediocre all around so I don't think this is a problem exclusive to Sonic. Mario has this problem too, so does Rayman. Tropical Freeze is the only platformer I'd argue had some pretty good bosses (no coincidence since Retro also made the greatest boss battle of all time with Prime 2's Quadraxis), but even then many people will argue that some of those bosses went on too long. When I think of my favorite bosses in video games, almost none of them are from platformers.