Welcome back! Well most important chages were those that you pointed out, they added friendship too.
Most moves are working now, and there are TMs. There are also some move tutors around. And there are many changes in evolutionary methods (check the wiki out, but for instance golbat evolves via friendship now). I think eevee is able to evolve to flareon/vaporeon/jolteon/espeon/umbreon now but I could be wrong. Gender-linked evos like ralts evo or snorunt's are now possible.
Shiny pokes captured on the wild are 20+ iv now, and there has been several changes to spawns elsewhere (don't go looking for no snorlax in route 12 no more for instance).
They added held items, and also some pokes drop items now (like magnemite and murkrow).
Other than that... /help channel is the new /all channel, and you can link your pokes directly in the chat by holding shift and left clicking on the poke. IV and EV information of your pokes is easily available now too, right from mouseover you can get that!
Place with highest lvl pokes I think is the inner level of Cerulean Cave. I don't know if dragon's den new quest was available two years ago tbh but bagon is catchable in the cave. I don't know if I missed anything major, please ask away if you find something odd! hahaha
EDIT: Jinji beat me for a few minutes but leaving it here just in case any of us missed stuff, which would be me in any case so I dunno... O