Yes I am still continuing it.
1) Yes there will be a story. Although I haven't really started thinking about it much.
2) I don't think it will be standard. The main trainer is not always just a young boy or girl eager to becoming a Pokemon Master. You can pick many different trainer types from old men to old women. Therefore the story wouldn't work like it normally does. However I think there will be similar elements such as defeating the bad guys, etc.
3) Starter Pokemon hasn't been decided yet. I have toyed around with the idea of a random starter such as picking a Fire type you either get a Cyndaquil, Charmander, Torchic, or Chimchar, etc. Also thought about the starting quest choices can affect it as well. So for instance you accomplish X optional task, or you answer the NPC's in specific ways, you get a higher chance of getting a certain Pokemon. That sorta thing, but I am not sure the best way just yet.
4) As far as music it will be a combo of various Pokemon games, anime, and custom probably.
5) Yeah there will be some special Pokemon not available normally and must be got through events, rare quests, or special means.
6) Yup you will have an account and username.