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Hmm that's very interesting. Either the legendaries that you can see are unique to your trainer ID or something like that, or to a region, or just seen on different days but i doubt it. Will be monitoring this until somebody can confirm.
Did they really show you Groudon?
There are three café's, and I've visited each one almost every day and the only legendaries I've seen there are Raikou, Entei and Suicune. I'm playing Pokémon Y for the record. Every time I try to enter now the guy informs me that there are no further pokédex...
I read somewhere that when they usually prolong the weather effect from 5 to 8 turns, having one on a pokemon with drizzle/drought/sand stream/snow warning increases the duration from 5 to 10 turns. Need confirmation on this.