Every chapter is great in its own way, but if I had to pick one as a favorite, it would probably be Ruby and Sapphire. I might be biased towards Hoenn since my first Pokemon game was Ruby, but even without the bias, I genuinely think it's a great chapter with strong characterization for the protagonists. Speaking of which, it also started the trend in the manga of "dual protagonists". Previous chapters had multiple DexHolders but only one of them was the clear main protagonist of each chapter. Ruby and Sapphire both have about the same amount of screentime and character development in their chapter so they're the first proper "dual protagonists" of the series.