Game balance is, an elusive beast, there's no getting around it. You're never going to perfectly balance the different player characters against each other, unless you do away with player choice and random elements like ability scores.
But from a GM standpoint, it becomes very difficult to handle a party with wildly disparate strengths and weaknesses. A lot of systems devote time and energy to try and keep things on a relatively even keel. Others do not.
So while I loved the idea of Palladium games, for example, in every game I played, there was always one guy left at the bottom of the curve, struggling to keep up with the relative demigods he found himself adventuring with.
Like I said, the player in me goes "wow, look at all these toys!", but the GM in me goes "but somebody is going to end up being a sidekick".
Now some people might enjoy that role, but I've not encountered many.
As this thread is about opinions, things we love but know are flawed, I'm ok with calling them bad. Even if others disagree- I mean, a few posters here bought Street Fighter and loved it.
I bought it and while the combats were exciting and tactical, the out of combat part of the game felt lacking. There wasn't any particular reason to not specialize in Physical Attributes or those Abilities that made you a better fighter.
The rules sort of fell apart if you had to fight multiple opponents, as they were clearly made with the idea that everyone gets one action a turn. A few special moves could hit multiple foes, but these weren't common.
In the end, my group abandoned the game, and those books never saw the light of day again (I actually have no idea where they all got to!).
So, based on my experience, I could call the game bad. Maybe a better way to phrase things would be "favorite flawed games"?