Sorry for not answering in a while.
Yes there will be missions, and yes those pokemon should be available to catch in the wild.
I am currently working on the pokedex and MY NEW TEAM MEMBER is coding the Battle system.
Welcome the new coder, who remains nameless to help me and the team! He is the only other coder apart from me and he is helping immensely.
Just so you know how hard this is, I am coding the pokedex at the moment, and I have over 4900 lines of code, all with info of every pokemon. I am slowly progressing through it all with a friends help, how if continues to help will be an official team member also :). We have to read all info of about 500 pokemon....
This is just the baseline code. We are however zooming through this with hundreds of lines of code completed each day, but my nameless coder is working solely on the battle system, which is a monsterous task, and I will be helping him soon.
Keep in mind this is so huge I can't explain it, and will probably take 30 hours straight at the computer for me and my friend to complete the pokedex, then we will finish the battle system. New demo coming soon, maybe 2 weeks or so.