Maybe add in something where you can get berries from using cut on trees. It would work like how rocksmash can find items. Also maybe add the chance to find a pokemon when using cut. Pretty much the same effect as headbutt.
As for two regions how about start in Kanto then go to Johto. Maybe have an event where when you go to Mt. Silver Gold will show up and battle you which puts you in the place of Red when he was battled in G/S/C. After that battle it could trigger for the time skip to happen and you can go back and re-battle the kanto gyms who all have new teams higher levels the works. The elite four of the time skip could be rivals or trainers from the past games that have now taken spots of the e4. Maybe have some more contests for catching pokemon and getting prizes. Have bug catching, Fishing, Ghost Hunt. Tournaments where you enter one pokemon of a type. Have a chance for pokemon to abandon their trainer based on happiness. Maybe also have trainers you fight a random chance that they will give you one of their pokemon to train. Have team rocket use pokemon that you believe they would steal like taruos, kangaskahan, Scyther, Gengar, Golem, etc. Sure they are grunts but I'm sure they could do better than over leveled zubat and ratacate.
