Yeah, I think it's due to availability.
For example:
Code:
- Mareep: Only available in Hoenn Safari Zone, post-Elite Four, when it's hard to train. Now available common as much to fight Falkner with for your first badge in Johto!
- Stantler: Like Mareep, only incredibly rare.
- Heracross: Available in LeafGreen, but rare. Even rarer in Sinnoh (yet Barry has that AND Munchlax). Commoner in Johto.
- Remoraid: Fairly easy to find in 3rd Generation, albeit post-E4. Common as muck in Sinnoh. Suddenly rare in Johto, so less common.
- Marill: Common in 3rd Gen. and Sinnoh. Suddenly rare in Johto, so, becomes less used. However, due to being Johto's equivalent to Pikachu, its' value increases and many people also search for it.
At least, that's my opinion. :D