Totally agree with you OP, it's a serious oversight and it does matter to a lot of us. Here's the main thread on this, and related issues, that necessitate either resetting our 1.0 characters back to their 1.0 backup or implementing features so we can correct such mistakes:
http://forum.square-enix.com/ffxiv/t...y-char!/page13

Just like you, many of us didn't expect this when we imported and are now sorely disappointed that we can't experience the story from the beginning in the cities we love. You should probably submit a support ticket or email as many of us have so SE is aware this is something a lot of people care about and would like a solution for. Understandably, it's not a major issue for them right now, but hopefully we can at least get the ball rolling.