There are a couple of good guest houses in Causeway Bay - in fact right outside one of the airport bus stops. They are not your 'chungking' style guest houses but actually quite comfortable. You can visit
www.asiaxpat.com.hk and there is quite a bit of info on them in some of the forums.
One thing about the IBIS is that you can catch the ferry from directly opposite the hotel to Hung Hom and then from there only a short bus/taxi ride to the Hung Hom KCR Station to catch the train to Shenzhen - no messing about with MTR connections etc...