They swapped the names of Salamence and Flygon at the last moment: Bagon - Shelgon - Flygon
The Hydreigon line was supposed to resemble tanks but this got dropped during development
Butterfree and Venomoth got swapped evolutionary lines at the last moment
Kangaskhan was supposed to be the final evolution of Marowak
The first gen pokemon basically ALL got their English names changed at the last moment. Thank God, because the original names got leaked and they were all atrocious (Koffing and Weezing were called Ny and La, Machoke was called Karatee)