Have any of these indie Pokemon clones ever been any good?
As someone who has played an embarrassing amount of them, I can honestly say
no with total certainty.
Not a single one on the App Store is good (which is a given, but a very necessary clarification seeing as the Nexomon series is multi-platform and on there alongside many others) save for maybe Micromon which had the bonus of being released 10+ years ago and no longer available (it has a very very shitty rerelease that's significantly more unstable, but the original was probably the best Pokémon clone on the App market for some time). Almost every single one made via Kickstarter (90% of them) is bad.
What you said is exactly right and it pains me to see a bunch of snooty former-Pokémon-fans taking their rage against the series and deciding to use it to JUST MAKE POKEMON AGAIN but with infinitely more shallow aspects in every regard. They add fan-favorite features like Nuzlocke modes or following mon into their shitty clones while neglecting to remember why people liked those in the first place (self-imposed rules that facilitate story-telling and substantial interactivity with your mons on the overworld). They copy Pokémon's battle style wholesale while adding a singular gimmick solely to differentiate it every single fucking time (be it Fusion, ATB combat with everything else remaining identical, or move-exclusive types in Cassette Beasts, Kindred Fates, and Coromon respectively) and expect that to sell. They add the -mon suffix to their name despite it making no goddamn sense (Nexomon, Coromon, Ploxmons, etc).
These people will whine about being branded clones, but then you look at their gameplay and it's
literally all you can see. They graft their own shitty homemade skins onto Pokémon's corpse and then get upset when people see the rotting flesh behind the bad arthouse painting. They circlejerk the greatness of their own genre so hard that they only post their game updates in a discord server centered around a single shitty youtuber milking this gold rush for everything it's worth, then get offended when you mention that the vast majority of these games do fuck-all to advance the genre and are clearly just trying to ride the trend for easy cash.
As of now, all this genre consists of is people shallowly remaking Pokémon with less depth, 0 attention to worldbuilding or tone, significantly worse creature designs and shittier names. There's a few outstanding franchises that've come before all this stupidity: SMT (and Persona), DQM, YKW, Pokémon itself, Fossil Fighters, and a few select Digimon games come to mind; but EVERYTHING else is trash and not worth your time.
Unrelated fun facts: that aforementioned discord server was so desperate to qualify things as part of the genre that Balan Fucking Wonderworld had its own channel underneath the "montaming games" category pre-release because of its costumes. The server is also full of idiots who can't discern obvious tracing from normal art lmao.