Find your niche.
Ruby! I like both teams but I always thought that Team Aqua was a good group and was meant to help you throughout the game like they did in Ruby. Although that was soon thrown out of the window come Emerald, when Team Aqua getting the base near Lilycove made so much sense as well as the pivotal roles of the troublemaking team from the dual versions.
Plus I liked Groudon's design a lot. Also I thought the red accents in the main protagonists' original clothing meant that Ruby was the actual intended main version instead of Sapphire, so yeah.
Still, I just have to add since apparently majority liked the third version the most, Emerald's really good! I love the additions, the condensed storyline as well as having to face both teams and seeing an actual cutscene with the Weather Trio. The Battle Frontier was also a welcome addition!