Rick and Morty is one of the oddest comedies made, in part because it exists as a satirical glance at science fiction as a collective genre. Drawing from science fiction like Back to the Future, Doctor Who, and many others, the series presents the cynical adventures of the alcoholic, misanthropic Rick, whose anti-social behavior causes everyone around him unending pain, but because he's smart he feels he can just get away with being a toxic person.
One of the more bizarre ideas presented, due in part to its multiverse and inter-dimensional hi-jinks, is the Council of Ricks, a council of alternate reality Ricks who craft an inter-dimensional league to govern their own actions. This is an idea so seemingly bizarre it can't have any equivalent in modern fiction. But there is in the form of the Interdimensional Council of Reeds, a council comprised not of Ricks but of the Fantastic Four's Reed Richards's -- Marvel's greatest scientist. Both are councils comprised of arrogant scientists who believe themselves "above it all," but which one is actually worse?
The Origins of the Councils
The origins of the Council of Ricks is handwaved in context as just a bunch of Ricks getting together and forming an alliance. As with all things in Rick and Morty, we're expected to just accept this happened and go with it. Apparently, a different interdimensional council used to reside in the Citadel from which they rule, but the Ricks have at some point taken over without much difficulty. First consisting of six Ricks, it soon grew. Though one Rick stood apart from the Council -- the "Rogue." This is Rick C-137 -- the main Rick from the series.
On the other hand, the Interdimensional Council of Reeds was assembled by three Reeds who had managed to assemble the Infinity Gauntlets in their own reality, they concluded it would be necessary to improve the greater reality of the multi-verse. The council decides what is best for the greater whole of the universe, repopulating abandoned planet and hoping to end hunger. However, in order to perform its tasks, the Reeds that comprise the council need to abandon their reality, often to its own horrific devices.
One oddity is that, in the Council of Ricks, each Rick uses its Morty as a defense, seeing them as an expendable resource for personal gain. On the other hand, every Reed has seen their duty to serve the multiverse as more important than any one person in their own reality. Neither of these are too shocking, given the two characters' sense of sociopathic apathy toward those around them. (That, of course, is more obvious in Rick, but never forget that Earth-616's Reed Richards also constructed a prison in the Negative Zone during Civil War in which Reed's fellow superhero companions would be locked up.)
It is also important to note that all members of the Council of Reeds had their sons, Nathaniel, stripped from them, which further pushed them down a path of self-isolation and obsession.
What Do They Do?
The Council of Ricks mainly just govern one another and their own activities. They hold their own accountable for their actions. If this seems like a lot of hoopla over a very small field of authority, you'd be right. The Council of Ricks, by its very nature, is an absurd concept. It only governs other Ricks. That said, the Ricks remain among the smartest people in reality, and many -- most notably our Rick -- has caused so many problems for society that it's not out-of-line to say Rick C-137 needs restraining.
On the other hand, the Council of Reeds exists to help the multiverse. They use their immense knowledge of science and technology to aid every and all multiverse -- as they see fit. Keep in mind, this is a council comprised of Reed Richards, a man who often breaks the laws of physics when he sees fit. As such, they often will often take justice into their own hands, dealing with interdimensional versions of Doctor Doom in the best way they consider it.
Also, as a result of abandoning all their loved ones, many of the people from the various multiverses the Reeds come from either resent or forget that Reed ever existed at all. So while each Reed might be serving as a super-scientist for all reality, they're inflicting so much pain on those around them that it eventually numbs them to feeling anything toward Reed.
The Opposition
Both our Rick and Reed oppose the council, though for very different reasons. It is in this sense that we can truly understand which council is worse or better than the other.
Rick C-137 opposes the Council because he sees them as stooges who just want to ignore their true nature. Rick is an iconoclast by his very nature. He tramples on established traditions and customs with joy. Of course, all of this is a veil to hide his true emotional pain. Rick is not a hero, nor is he a particularly happy person. Due to his own self-imposed isolation, he pushes everyone else away. These actions resulted in both the Council of Ricks and Rick C-137 attempt to murder one another.
On the other hand, Reed Richards opposes the Council of Reeds because he's a slightly less self-isolated person. Because his Nathaniel was never taken, this Reed retained some degree of humanity, that kept him from wanting to join the Council of Reeds. This, combined with a conflict with the Celestials, resulted in the council being ultimately demolished.
Reed had later confrontations with surviving Reeds, but ultimately it would be some time before a new Reed rose to reassemble the Council of Reeds. That someone turned out to be the Reed Richards from Earth-1610 -- Ultimate Reed Richards, now known as the Maker. So the Council is now led by a symbiote wielding madman, making it infinitely worse than anything Rick Sanchez could ever imagine doing. to give you some perspective, the Council of Reeds played a role in the Absolute Carnage event, with the Maker holding off all of the Avengers while wearing his symbiote amalgamation.
So yes, especially under the rule of the Maker, the Council of Reeds is way worse than the Council of Ricks.