I had forgotten about the free games from the Ambassador Promotion, that seems like a huge plus to me. You got a ton of great games which isn't on the normal Virtual Console (at least not yet). Metroid Fusion, Fire Emblem:TSS and Zelda:MC are three games that I really want to play.
You were really lucky with the shiny spreads for one of your IDs at least. Getting a Modest Flawless spread as shiny without an ID/SID abuse is amazing.
Darkrai and Shaymin would be nice to RNG, but I guess you are right about legal wondercards being impossible to get this long after the events. At least we got a Darkrai event for 5th gen, hopefully we'll get one for Shaymin as well.
The version mascots are really cool as shinies for the most part, so I understand that you want to get them. I would love to get all of the remaining legendaries as shinies as well (at the moment, I have Articuno, Mewtwo, Entei, Lugia, Latias, Kyogre and Palkia). Though I can't bring myself to restart one of my 4th gen games, so it will probably never happen.