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Ok, this is an incredibly hot topic here it seems and I just wanted to add my 2 cents cause I feel I've got it figured out.
Keep in mind I'm not saying whether it's a definitively good or bad thing, just why I think gamefreak went this route when making gen 3
Essentially, it all comes down to pacing. In gen 2, the pace is decidedly slow. Due to the lack of any real story outside of your own as a pokemon trainer there's never any narrative momentum (get used to this term) going on for any longer than a single self contained story event like the radio tower, and because of this the game feels a lot more like an episodic adventure where each day brings new experiences to be had. This ties into the non-linearity, it's way more about doing things when you want to rather than when the games wants you to.
This all meshes extremely well with the day and night cycle, the adventure is slowly paced out, and the game/world design compliment this. Progressing through the world too quickly actively hurts the experience, since you could be missing out on a potential rare night time exclusive pokemon in an area, or a cool event that's only available on some days. This only works BECAUSE the lack of narrative momentum means you have no reason to be rushing to begin with.