So I lost track of time between playing 2.01 and work, I see we are on 2.3 already, will finish my dex and then shift over for a more fun play instead of a completionist one.
@restest I have noticed a few things getting a complete dex, wonder trade system excludes legendary but I guess it's meant to, however it also seems to not give a Paras, Aerodactyl and Relicanth. It will give a very low level probopass. I recall comments about cheesing wonder trade, I know emulators are what they are but it's still possible on original hardware, there are 2 ways I can think to stop it. Then I am collecting legendaries, I am currently after regies and struggling with some translations, the chart you used would be a great addition in the faq, suicune and entei did not disappear after catching them, I will need to recheck Raikou.
Probably the weirdest of the legendaries was mew two, when reaching the water, i can just walk on the water but cannot walk onto the island he is on. I got surf to work if I recall from the island to the left but then can't get off or any interaction on the island and if I go back to where I came from where I start walking on water it will just surf on land. I used the debug menu to disable collision to reach the island, catch them and ad to do the same to get back as I couldn't initiate surf. Perhaps this is meant to happen, if not perhaps you can a creative solution is to do some event, when you get to the water you get pushed back by a mysterious force but having mew, or the birds or something he will come to you or something