I'm not a big fan of it - when I was a kid I only got games at christmas and my birthday pretty much, and they're 14 days apart in December so I usually missed all the events. I think it was slightly better from Gen IV onwards when they were distributed online rather than in-person but it still excludes a lot of people from being able to capture all the pokémon - I personally think it should be possible to obtain every single pokémon introduced in a generation between the 2 paired games (especially now we haven't had 3rd versions for a couple of generations).
My favourite in-game events I've experienced though...probably the ones in HgSs - I have the event Pichu, Celebi and Arceus - being able to battle Giovanni again is great and also helps wrap up a few unanswered questions, and actually seeing Arceus create life is pretty cool as well. The Darkrai and Shaymin events in Platinum were pretty cool as well. I never understood why if Darkrai and Cresselia are a duo and the former clearly affects an individual in the games, you wouldn't be able to get both. Seeing Shaymin's tangible effect on the land is also nice even if I would rather have had more Prof. Rowan rather than Prof. Oak appearing yet again.