Yup, there's no wrong way to run it. :) I like keeping caught legendaries in an untouched form in addition to Events, so provided I have inventory room I do just that. When I catch the Uxie family in Sinnoh, I'll probably keep clones of the original trio there and the originals will join my party, with clones moving between systems (very likely without using them in Black, or in White 2, just for trading purposes).
What's interesting is that I don't try to get every single Event; I don't have to have a 2002 Special Event "insert here" available only at "insert store" locations in Korea. I just want at least one of each Pokémon that I can share with someone, and where possible, one Event/Shiny and one standard version to satisfy both preferences. I mean, I'm going to keep one of each legendary inside the "Dex" boxes (1-14 right now), and I have two separate "Legends" boxes (ran out of naming space, 8 characters only) where clones hang out in (or will once I have every single one cloned, first two gens. are generally done this way already except for the missing ones).
So...while my primary focus will be on a breding center, and that's where most of my work will go (trying to create perfect babies in every species legally without RNGing or anything like that, except for Phiones which can't breed on their own, meaning I can only guarantee one perfect EV stat), legendaries and Events will still be featured separately in the shop. I'll be looking at other trade shops for inspiration, but as for actual shop design, that is something I could also use help with. Probably won't revamp it at some point either; may as well open a new shop if you want to revamp. LMAO