Nice plot. Not outrageously improbable. Very well-written. xD *thumbs up* Doesn't tell you much, but that's okay! Hey, is your missing father THE LEADER OF THE EVIL TEAM? That would make for a great "LUKE I AM YOUR FATHER" moment.
You did not just say time travel. Oh my god, you did. AAAH
I have no warm feelings towards any of the canon characters, so I vote for none of them appearing, unless it's for humour and/or completely unrelated to the story. IE, wack pairings of everybody's most and least favourite characters. (Actually, I'd really like to see that.)
As for the starter, I think it should be very carefully chosen. First, it shouldn't be ineffective against wild Pokemon on the first route. If they're all rattata and pidgey, don't give the player a Gastly. XD Also, it shouldn't be a crappy Pokemon. Players should have a reason to like their starter. Don't go for Eevee, though, that's overdone (also Eevee is crappy in battles). If the starter evolves with an evolutionary stone, make sure it's easily available, say, from an NPC. Houndour might be a good choice. It isn't totally overused. That, or Growlithe. It's more common, but everyone likes Growlithe.
Since your game is going to feature canon maps, make sure your maps are in the 'official' style. For instance, in your screenshot, there's a lot of extra space between buildings. It looks rather lonely. Put them closer together and your map will look more official. :) Also, you have a whole range of house styles in one town. Is that a particular feature of your region? I'd recommend sticking with one house style per town. It's less realistic, but it gives each town a certain flavour.
*Edit: Dude, you have to crop your screenshot. It's stretching the screen. :<