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Hey Spherical Ice, Talonflame's sprite in the Pokemon menu is glitching, and for some reason, the sounds (when you interact with something, when you open the menu, etc.) are a lot quieter than the music.
Did you turn on RealTimeClock in your emulator?
Wait for nighttime (I believe 8pm), then go to the path below Lola's gym. An event should activate there, involving the Rockets. Follow them to the deepest end of Forslorn Rainforest, and something will happen. Thereafter, Lola should be back in...
Suicune learned the move Roar, and he's at Level 20. You're not supposed to be able to catch it yet, given your current team. This Suicune makes a cameo appearance in that route, and will appear later in the storyline. So you're only supposed to catch it much later in the game. Not in Beta 2 yet...
The current beta (Beta 2.5) stops at right before you can go to Pokewood City. That's roughly about half of the first region. The second region is not in-game yet. Beta 3 will feature more of the first region and a small part of the second region.
This hack is still alive! A few posts back, FrozenInferno said that he's going to release Beta 3 around August 20. There have also been regular checkpoint updates (if you refer to the 1st post) and new screenshots in the making of Beta 3.
Go to Valencia Island's Pokemon Center, and interact with the giant machine to the right. That is the "portal" which leads you to the bonus chapter area.
Regarding the Town Map (and the Poketch map app), some areas are not registered in the map at first (such as Newmoon Island, Fullmoon Island, etc.). They only appear after you have first gone to that place. Are you going to implement this, or are you just going to put the full map in?
How will the Pokephone work? Does it have features like the Pokegear? The concept of texting is cool. I'm very interested to see how this will turn out!
The 4th Gym Leader is in Ignite Heights. There's a cave (with the GYM sign above it) where it's dark and can't be lighted up. You have to solve a certain puzzle in there to go into the Gym Leader's room.