Right, firstly...
If this is not a remake, you still should try and stick to the Pokemon Story. RSE takes place at the same time as FRLG/RBY, therefore Brendan completed his journey three years before Gold started his. If this isn't a remake and you're going to include Brendan, you'd be better off making a new player/hero altogether.
I don't think you should battle Brendan there, since he's moving to Hoenn, he shouldn't be battled until you go to Hoenn. (Obviously what you're trying to do to be original is replace Kanto with Hoenn, so as the "Epic Battle" of the game, you should battle Brendan at the end). Create new heros, and a new Johto Rival- let Brendan be a friend.
Anyway, secondly...
Above, you admitted to basing the New Bark map off the Shiny Gold one- and that you've now edited it.
I now know why- sorry to say, but you really need to work on mapping. You're trying to impress everyone with what's included in the hack, but.. It's nothing that special, to be honest.
(btw, that Cianwood map, and the Route next to New Bark, they're both from Shiny Gold, I'm pretty sure). There is a huge contrast in the mapping styles of the New Bark, Route, and Cianwood map, and Joenn Path's map- which is obviously the only map you've done yourself.
1. The Joenn Path map is too straight. Route's need to have a bit more.. Twists and such. Add some trees, too. But, read on...
2. As someone has said, the mountain placement is not physically possible- they're joining up incorrectly, you need to add more layers, etc.
3. Make the whole thing twice, if not three times as long. It's joining Johto and Hoenn, and it shouldn't be properly accessible until you've got the 8th badge. Look at Tojoh falls/the Kanto Route that leads to Johto. You can surf across to Kanto when you've got the fourth badge, but you can't go any further til you get Waterfall, and beat Claire.
From you're map, Hoenn is fully accessible to the Player when they reach Cianwood. Ok, so what you need to do is..
1. Make that map a lot longer. Seriously, go nuts here.
2. Add the need to use a few HMs, with perhaps a Waterfall at the end of the route or something, to stop the Player from being able to get too close to Hoenn early in the game.
3. Add some more trees, and fix up the mountain placement.
(I highly recommend you read a mapping tutorial, and think before you map. You don't seem to understand how to use certain tiles, and that can result in bad, illogical maps like Joenn Path here).
Sorry for the long post, and I hope I didn't offend you or your work here (but seriously... Ditch the Shiny Gold maps, man. Try harder to be original).
