Some of you may know that some of the people who worked on Earthbound and with Ape Inc. went on to make Pokemon. If you look carefully, especially in Gen 1, you can notice a lot of throwbacks.
1. Mewtwo = Giygas theory Both are powerful psychic entities. Giygas' sprite in Mother (Earthbound Zero) looks vaguely similar to Mewtwo's sprite.
2. Pokey/Porky Minch = Blue theory Both are rivals you encounter at various points in the game. Both consistently taunt you and are always one step ahead. Both were your neighbor and childhood friend. Both are featured in the final battle. Blue can be seen as Pokey/Porky if, instead of staying a jerk, matured and reconciled with his rival.
3. 8 Your Sanctuaries = 8 Pokemon Gyms Same with 8 melodies and 8 badges. Not much to expand here.
4. 4th city is a metropolis / Plant Bosses Fourside and Celadon City. Really stretching it though especially since you get the Fourside melody 5th. The fourth badge and correct 4th Your Sanctuary (Rainy Circle in Winters) involve a battle against plants (Erika's grass pokemon and Shrooom!)
Anyway, that's all I got. Any other thoughts?
If you need instructions on how to get through the hotels, be sure to check the enclosed instruction book