If I remember correctly, Magikarp was removed E12, and most things were removed / pushed back in 10.5 / 11, which is why most people ask for Episode 9 downloads.
A list I can think of for removed / pushed back Pokemon are:
Magikarp (Removed)
Starly (Formerly Onyx Rooftop, now Route 3/4 [i think])
Abra (Formerly trade in return for Bibarel, unsure what you get now, unsure of location)
Ralts (Replaced with Espurr, now Corrupted Pokeball)
Zubat (Formerly Abandoned Railnet, now Byxbysion Tunnels / Glitch City)
Gastly (Replaced with Misdreavus, Removed)
Vulpix (Formerly Obsidia Salon, replaced with Litleo, unsure of location)
Elekid (Formerly Beryl Rooftop, replaced with Helioptile, now in Calcenon City)
Magby (Formerly Abandoned Railnet, replaced with Pansear, now in Calcenon City)
Shroomish (Formerly Azurine Island, now in 1/18 egg)
Togepi (Formerly Coral Ward quiz, now in 1/18 egg)
Riolu (Formerly Apophyll Academy, replaced with Darumaka, now in Ametrine City)
Mudkip (Starter) (Byxbysion Wasteland, replaced with Squirtle)
Bulbasaur (Starter) (Formerly Azurine Island, replaced with Chikorita)
Azurill (Formerly trade in return for a Growlithe, now in 1/18 egg)
Drillbur (Formerly Tanzan Mtn. Depths, now in 1/18 egg)
I'm sure I'm missing lots more, but these are what I recall from the top of my head.