Semantics.
Reverse Flash/Professor Zoom
In his classic origin (The Flash vol.1 #139):
Eobard Thawne is a man with ambitions of becoming the greatest criminal of all time. He finds The Flash's speed suit in a time capsule. Takes it home sets up some lab equipment and taps into it's residual speed force wave patterns which he then amplifies so that he could have super speed whenever he wears it.
The Flash
was his favorite character in history. Only because he admired his super speed. He hated him otherwise from the very beginning. Simply because The Flash stood for law and justice while Thawne would stand for the reverse.
In his most modern comic book origin (The Flash vol. 3 #8, Flashpoint: Reverse Flash)
Eobard Thawne is a student of science obsessed with finding out the secrets of time. Because he had a sibling he had to often care after thanks to the laws of his society he fell behind in his studies. He had applied to The Flash museum "to become a student of the mysterious energy source that once powered the proud legion of speedsters. The speed force."
He was rejected by The Flash museum. Without any authorization he hacked into the historical records that spoke on the speed force on his own. His kid brother who he had grown to despise had become a cop of their time. He found Eobard in the middle of his illegal acts and busted him. Later on one of the first things he did when he could finally use super speed was erase him out of existence.
Once he became an only child and redid his history he had more time to dedicate to his speed force and time obsession and studies. He dedicated his entire life to studying and earned a place among the scientific elite of The Flash museum.
He became the ultimate authority on The Flash. Then when he was beaten to the punch in finding the secrets of the speed force he took out the professor responsible for that and became the only authority on the secrets of the speed force afterward.
He finds Barry Allen's speed suit in a time capsule and then syphons residual speed force energy and recreates the accident that created The Flash. Becoming The Flash of the 25th Century.
He was someone that as The Flash of the 25th Century would do things like push a girl off a rooftop with superspeed just to "rescue her" from falling. He eventually meets and ends up despising Barry Allen who after a trip to the 25th century and seeing what Thawne was really about stopped him and handed him over to the authorities. As you can see here in this spoiler box:
That's when he declared revenge in reverse. However that is just another excuse for what was already pre-existing vile behavior.
When a girl rejected his advances in the past he went back in time after becoming a speedster and made her catatonic. He's a guy who is manipulative and cold. Calculating and very conniving. He's egomaniacal and sociopathic does whatever it takes to accompish his own goals and complete his selfish agenda by any means.
Those are themes replicated in his counterpart in this TV adaptation. Key word is themes so again just because the details are presented differently he's no less layered than his Dr. Wells incarnation. It's an adaptation doing what it's supposed to do remixing the fundamentals of a character and presenting them in a way that fits their own narrative.
The Joker
This is a man obsessed with crime and chaos much the same way Batman is obsessed with justice and order. He is not so much obsessed with Batman as he is with the mind games he plays with him. However all that stems from his true obsessions: crime and disorder.
In his more definitive origins whether it's Bill Finger's golden age one from Detective Comics vol. 1 #168 or his more recent one in Scott Snyder's previous Batman arc (Zero Year) he is already a man presented as being fascinated with theatricality, disorder and crime before Batman he even comes across Batman.
Yes once he finally meets Batman he ends up becoming amused and intrigued by him. However it's not to the point that he couldn't exist without him in any incarnation or will always want to keep him around for his enjoyment.
Matter of fact one of the conceits of the most recent Joker story going on right now (Endgame) is that he is tired of wasting time toying around with Batman. He's no longer amused and wants to nip their relationship in the bud once and for all.
He's a wildcard and malleable. One minute he could think Batman is dead and become sane or pose as a criminal specialist (Oberon Sexton). Or he could continue being what he is well into the future with or without a Batman to be his foil. He is random and unpredictable and very chaotic like that.
So looking at both characters fundamentally that way there is no way they could be interchangeable. Even the way the execute their menace is different let alone their entire psychology.
So to try to group them together just because they're both "obsessed" even though obsession itself is a very multifaceted concept that won't apply to 2 individuals in the same way is in my opinion selling the characters a bit short.
They have more depth than that.