What prompts me to ask this is mostly the gym leader teams. They are made primarily of Generation I Pokemon, with no gym leader having more than 1 Johto Pokemon. In fact, the only Johto Pokemon used by any of the Johto gym leaders are Whitney's Miltank, Jasmine's Steelix, Pryce's Piloswine, and Clair's Kingdra. Out of the 8 gym leaders, there were only 4 Johto Pokemon on their teams. There were plenty of options they could have taken too. For example, instead of either Pidgey or Pidgeotto, which we had already seen more times than we would have liked to in the previous game and in this one, Falkner could have used Hoothoot, Murkrow, or Natu. Bugsy had Heracross (which may have been too powerful for that point in the game), Ledyba/Ledian, Spinarak/Ariados, Shuckle, Pineco at his disposal. But he settled for Kakuna, Metapod, and Scyther. Scyther is a cool Pokemon and deserved a spot on his team I believe, but the Metapod and Kakuna were just dead weight. Morty could have used Misdreavus, Pryce could have used Sneasel, the list goes on.
Another example I'd like to bring up is the fact that many Johto Pokemon were very rare and only found in one or two locations, many in the Kanto region post-E4. Misdreavus can only be found in Mt. Silver with the added obstacle of only making it obtainable at night. By this point in the game, it would not be useful to catch and train for in-game purposes anyway. In Gold and Silver, Houndour could only be found on Route 7, at night, with a 5% encounter rate. This was bumped up to 20% in Crystal, but this is still very late in the game for a relatively mediocre Pokemon.
So to go back to my original question, was Game Freak afraid to focus on the new Pokemon in the games over the previous generation's, and if so, why would this be?