Can't answer 1 and 2, but...
3. It's implied that the events in Hoenn (Primal Kyogre/Groudon and Delta Episode) created more mega-stones due to sharing similar circumstances to Kalos' distant past. If Mewtwo was created before ORAS, then his mega-stones could have formed during one of these plots (and then he took them with him to Kalos for XY).
4. Beginning to think that the harshest punishment in the pokemon world is a time-out, due to how rarely any villains ever see punishment.
If true law was upheld, Maxie and Archie would be incarcerated for grand scale eco-terrorism, Giovanni for taking a building hostage and unlawful experimentation, and Malva, Saturn, Colress, the Sages, N, those two girls whose names escape me in BW, and others would be still tried as accessories to a crime (or much worse).
Honestly, it's easier to count how many DID get arrested. All I can think of is Xerosic, Charon, the Sages (most later released/escaped), and Ghetsis (DID escape).
Not counting Colosseum/XD, just because I can't remember at the moment.