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So I think I've figured out a solution to the Diglett Cave dilemma.
1. I'll have this guy here block the cave off until you beat Brock, after which he will warn you that things might be tougher going this way. There's not gonna be level 30 Dugtrios anymore but it will still be higher level going that way than going via Mt Moon.
2. Cut will still be in the ship but Surge won't be blocked by a tree. If he was then you would have to go all the way to Bill's and back again which would kinda defeat the whole point of taking the tunnel at all
3. A rocket grunt will block the road east of Cerulean until Mt. Moon has been cleared, otherwise there would no reason to go there. I'll add and npc or two in Cerulean to point out that Team Rocket is there and that you should probably go check it out.
4. You can backtrack to Mt Moon from the east now, but that should be a given.
Anything incredibly stupid that I missed or did I cover my bases sensibly?