And like Nideous said I am willing to look at SUs a second time once it has been edited.
EDIT: Okay everybody, here's the info you need before you get started. Sorry it took so long. I just got the computer.
With Capturing Shadow/Regular Wild Pokemon: Pokemon from all regions have migrated over the years to the other regions. However, region-specific (or basically where they were originally shown in the games) are the most common. To Pokemon from other regions, unless captured from a Cipher agent or a gift, they can be found in the habitat that are similar to their original ones. Example: You can normally find Sewaddle in Pinwheel Forest. They would also be in Ilex. Got it? Wild Pokemon levels vary depending on the Route.
Purchasing new items: You start out with your basic journey kit, if you can afford it. However, because Johto and Kanto are very dangerous for trainers without the strongest members of the League Association, many marts have closed their doors. Goldenrod is one of the few that keeps their doors unlocked, as does Celadon. As such, goods are being sold in Pokemon Centers but there's a limited stock and clerks will not give stronger items to newbie trainers. As a side-note, whether you have a Pokedex is your choice.
Your first Purification Stone comes with your first Gym Badge. Your Badge can either come from a win, a tie, or if the battle is good enough despite a loss. That last option is from my judgement, as are Gym teams. Purifying your Pokemon completely can only work during the day and after the Pokemon's heart is opened again. Shadow Pokemon have at least one Shadow move, which I will replace (Egg or TM) once purification is complete. (You can give me a preference though )
TM and HM moves can be learned, however, it must be shown. TMs can be found on the ground, rarely, otherwise there are underground shops (expensive) that sell a few.
Cipher: It's EVERYWHERE! So you may be being watched, even you Cipher wannabes. After all, you could betray them. They may challenge you to a fight even. Be on your guard.
One last thing: Mewtwo is currently roaming the regions, as is Mew. The Association does not recommend capturing them. Cipher would enjoy it if you tried. After all, they may lead to the one Pokemon they need. Who is it? Should be obvious hehe.
That's all. Happy rping!