Miguel - Chrono Cross
This guy.... Few bosses in video games have caused as much frustration and intimidation as him. If we do not include any optional super-bosses then Miguel wins my vote for most hated boss in a video game. His backstory is that he is a close friend of the father of Serge. Miguel is also the father of one of his love interests. You meet him in one of the creepiest places in gaming history, The Dead Sea. It is basically a place frozen in time full of erased timelines that no longer exist and that is putting it in the simplest way possible. Miguel got placed there as its guardian before the game's main story takes place. It's bad enough having to defeat a friend of the family to get out of The Dead Sea. That's only the storyline reason. Now, let's get into the in-battle portion.
The battle goes on while a very sad tune plays that conveys not only how sad Serge must feel to battle a friend of his family, but also the importance of the battle. For most of the game Serge has an innate element of Holy, roughly 60% of the game. For the remaining portion of the game he has an innate element of Shadow for storyline reasons. Miguel is Holy. So guess which portion of the game you fight him in? The part when you're NOT Holy innate. To make matters worse, Holy is super effective against Shadow. Miguel uses extremely powerful Holy elemental attacks during the battle, one of which even resembles him weilding a lightsaber. Don't let his appearance fool you. This fight is as brutal as it gets when disregarding super-bosses. Unbelievably difficult for a little less than halfway into the game. No other boss in the game even touches his difficulty and few in other games do.