I am disappointed with gen 3 beating gen 1.
Me and you both bro. I don't understand it. lol
While I agree with this statement, you have to remember the qualities Gen. III brought to Pokemon.
Aesthetically - Some Pokemon from Gen. III were pretty great design-wise. I have no idea what the most common favorites are but I personally enjoyed Blaziken and Sharpedo a lot along with others. The Hoenn region was pretty nice. While one could argue to overuse of waterways, that's what the region was. Hoenn was also extremely diverse - cities, towns, forests, desert, mountains, and ocean. Neither Kanto or Johto had all those themes combined.
Competitively - Hoenn brought natures, adding more flavor to the competitive side of Pokemon. Hoenn also brought Salamence, our friendly neighborhood suspect. If you play Ubers, two of the most influential Pokemon derive from Hoenn: Kyogre and Groudon. Kyogre's usage speaks for itself, being called the "King of Ubers."
There are more, but those listed are viable reasons why some people prefer Gen. III over Gen. I.