Actually, I just moved the entire line to the end of the Pokedex. Ralts is now at #451, though I may have them reverted to their original positions in the final hack. You can actually catch Ralts in the alpha version in Route 30 at night (if I recall correctly). Any Pokemon with an evolution that jumps a generation, including those not part of gen 1 or 2, will be in the final hack (this includes Snorunt's line and Roselia's line, among others). Only ones I'm taking out are Azurill and Wynaut, as they are just baby Pokemon, and I plan on replacing the Incense items they require anyway.
Quick update: Just want to let you all know I'm still working on the game, but I've been experimenting and testing things to see what I'm able to do. I figured out how to do much more than I thought was possible when I first started this project. As such, despite what I had the security guard in the game say, I'm unfortunately not expecting a release to be ready before B2W2's official english release, though I still expect some sort of playable beta version to be ready this year. The list of Pokemon may change, but I'm not certain about anything yet... rest assured, every 1st, 2nd, and 5th gen Pokemon will be available no matter what. I've recently worked on updating the graphics as well, including new sprites for every 5th gen Pokemon, and including the new Pokemon overworlds from B2W2 (and updating some others Game Freak hadn't done). Here's a few new pictures of the graphics:
Some Pokemon with their old overworlds/The same Pokemon, but with their new overworlds/And some other Pokemon with their new battle sprites
Credits for updated overworlds: Game Freak, me
Credits for front sprites: KingOfThe-X-Roads on DeviantArt - link to the sprites
Credit for back sprites: Chaos Rush - link to thread
Make sure to follow my twitter page for updates on the hack. I also made a website, but I don't think I'm going to update that much. Twitter will have new info first most likely. Also make sure to e-mail me with any questions you may have! Or feel free to contact me any other way, though e-mail will be the quickest.