I have found a few more things I think may need to be looked at.
1) For the hell of it, I decided to sift through the Pokedex to see where Pokemon can be found. It shows Cyndaquil where Ilex Forest is. Yet exploring the Forest only revealed Oddish and Paras (also Caterpie if I recall correctly).
2) Route 34 has no wild Pokemon. Is this intentional or overlooked?
3) I have found Lv80 wild Heracross on the shore south of Owsuari City. Similar to the Missingno. glitch, you gotta surf the left shore.
4) In the Final Dungeon when you come across Nurse Joy standing behind a counter, all she does is thank you (for what!?). I'm assuming that she is supposed to heal your Pokemon. I think from a technical standpoint, this is the Nurse Joy that was in Silph Co. on RBY. Once you beat Giovanni in Silph, she doesn't heal your team anymore and all she does is thank you. Since the Warehouse is (from a technical point of view) Silph Co., defeating Giovanni in the Warehouse triggers the flag telling the nurse to not heal you. Would it be possible to either change the requirements for her giving the thank you text or replace that room with an unused Pokemon Center map?