It has been a while since I last read the completed chapters, so this will be highly based on my memories from when I last read them. I also tend to compare the manga to the story in the games, which influences my choices and opinions a fair bit.
My three favorites are the following:
G/S/C: The Johto story done right. The overall story is really interesting and engaging to follow (which can’t be said for the story in the Johto games). All three main characters are great, they are well written and each of them have a separate goal. I am especially fond of Silver, the manga does him so much justice after the games botched his whole character arc and development so hard. Team Rocket is an actual threat here, the Mask of Ice is a fantastic antagonist. The Gym Leaders as well as all the other major and minor characters are all great and memorable for the right reasons. The way the legendaries were implemented into the story was great too, with Suicune having a mini-arc of its own. The pacing is great as things happen fairly quickly, but never too fast. In the end, this was the Johto story I always dreamed of as a kid but that the games never gave me, and it is a good example of why I think Johto is at its best outside of the games.
R/S: The Hoenn story, but better than in the original Hoenn games. Another chapter with great pacing, an interesting story and memorable characters. I like how the relationship between Ruby and Sapphire develops during the story, and I am a big fan of the story arcs for some of the Pokémon (my top favorite is Feefee). Team Magma and Aqua were both well handled, the same goes for the legendaries, the Gym Leaders and the other important characters. Just a great chapter on the whole.
B/W: While the others are basically the game story but better, this is mostly just the game story retold in manga form. The B/W story was great as it is, there was no need to change much. This was very well done, both the story, the characters, the pacing and everything else. It is also memorable because this was the first chapter of the manga that I read, I usually like to start from the beginning when I get into something new, but I made an exception here since I was pretty tired of Kanto/Gen 1 at the time (this was in 2016) while I love Unova/Gen 5.
As for the others, I think several of them are good. FR/LG, Emerald, Platinum and X/Y are really great, they are my runner-ups. R/B was a nice start for the series, but a bit unstructured and incohesive. I think D/P had a solid story, but the pacing was very off. Yellow is one of my least favorites since I think Yellow and Lance as characters clash pretty hard in a bad way.
As for HG/SS, B2/W2, OR/AS, S/M/US/UM and S/S, I have only read through them once each, so I can’t really form an opinion on them. I will have to re-read them in the future to see how I feel about them. There’s also the ScaVio chapter, but it is still ongoing so I can’t speak for it yet (it has been pretty good so far, though). I have been meaning to read up on it now that there is an English fan-translation (don’t think I’m allowed to link, but it is on Mangadex), guess I should get it done soon...