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GOT IT! Errore region...I dunno, it seems to click somehow

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Starters-  Cyndaquil/Gible line, Cyndaquil subs, goes Fire -> Fire/Ground ->Fire/Ground, Chikorita/Starly line, Chikorita subs, goes Grass -> Grass/Flying -> Grass/Flying, and Totodile/Slakoth line, goes Water -> Water/Fighting -> Water/Fighting. Well, my idea, if we want to save time we can use existing lines.

Town List - Green Glade Village (starting town, prof. redwood), holds the lab, the social center/school where the players will start, of course on their first day of pokémon training and whatnot.
Arbor Trail connects GG Village to Virga Town, which is built around a large lake. Arbor Trail does not have grass obstructing the path, since obviously not everyone who wants to go to GG is a trainer, but obviously the grass and small forest at the sides of the trail are a good place to start training. Virga Town is where you'll get an Old Rod from a fisherman, which can only catch... Magikarp/Spinarak mixes, with Poison Sting, String Shot, and Splash. Water/Bug. First pokémon center and first gym leader, with... you guessed it, rock types. The mixes will have to be Geodude subs... possibly with Whismur? Uproar, Rock Throw, Astonish and Defense Curl, available for trade for a Magikarp/Spinirak at a house in town.
Afterwards, there is a branched path, one of which leads to a mysterious building (evil team hq, to be opened later?) with Shuppet mixes in the grass. Ooh, try Shuppet/Sandshrew. The path can be called, um... "Route vandalized sign with 'team whatsit' scribbled on it". The other way, Linkin Trail, leads to the next town, which has no gym but has a trainer arena, where trainers can settle fights together. Let's call it Linkin City. Oh! The arena can be remotely accessed via a Pokegear card that allows you to send pokemon over to fight from anywhere, much like a pc, after you've visited it. And yes, Pokegear is the best trainer gadget thingy. DIE, NAV AND ETCH! Removes the whole unrealistic aspect of the battle boards on the forums.
Then, we go to the next route, Basin Path, which goes down into a slope, which forms a dip that constantly fills with water. Water pokemon can be found by wading in, even without Surf! Of course there's a bridge...

Okay, that's all I have for now.