Unless I'm mistaken, I think only the Gold/Silver/Crystal games had a proper day/night cycle, but they were GameBoy Colour games. I don't remember any of the GBA games having day/night in them, but it's been a while since I last played them.
As for your original question though, Emerald is probably the best of the lot as a stand-alone game. It's a weird combination of the stories from Ruby and Sapphire (which were, shockingly, actually slightly different from one another), but the story carries on a bit longer afterwards from what I've read. It also has contests (largely irrelevant, but a fun distraction), berries (and the ability to grow them), the battle tower after you finish it, which is basically like a simplified version of how multiplayer fights really work (ie. all pokemon at the same level, only three per team, using taught moves), rather than the "beat 50,000 level 5 tentacool to level up until you're simply too powerful for a gym leader to beat you" mechanics of the singleplayer itself.
Fire Red and Leaf Green are quite good, in that they've remade the original GB games, but with all the updated system of the GBA games, but beyond just wanting to collect more monsters, or have a nostalgia trip down an old game, there's no reason to get it over the above three.
I fear I may have wasted too much of my life playing Pokemon games. Oh dear.