Currently for those on a tight budget, one of the ways to save money is to fly from KL to Johor Bahru, and then to travel overland to Singapore. This adds around 1 hour to the time to complete the trip into downtown Singapore, as you need to deal with the hassles of organizing a taxi or bus into Singapore. This detour is pretty straight forward after you have done it once, but a bit daunting, for newcomers to the route, with the biggest complaint being a lack of adequate, maps, signage or an impartial information desk to explain the process at Senai Airport. You also need to queue for a while at the Singapore border.
New rules will allow flights between the two cities which should start in Dec or January, and it is expected that there will be two flights a day by the low cost air carries Currently flights between Singapore and KL are available on Singapore Air and Malaysia Air, but the flights are premium priced, there is a real incentive to pay the extra as the train system, especially in Singapore, is really easy to use, and the cheapest and fastest way to move around Singapore regardless of the street traffic.
Speculation is that there will be a lot of interest by the governments of other capitol cites in region, that currently have restrictive polices on access, mainly to protect their flag carriers from value airlines like Tiger Air and Air Asia, two of the stronger regional budget airlines operating in the Asia region. Indonesia and its capitol city of Jakarta, it is hopeful, will see the advantages and create an atmosphere that encourages the budget carriers to operate, which will create more opportunities for business to flourish in the southern Asian region.
Recently between the cities with a stop to do some lets say scuba diving in Sipadan, it was very clear that something was remiss in that you could not fly from Singapore to Sipadan * to KL, but needed to fly either into Johor Bahru or KL, and add another flight segment or overland detour. You can bet that many travelers, through the southern Asian region would like to be able to book itineraries that could look like Bangkok to Phuket Thailand, to KL Malaysia to Sipadan in Borneo to Angeles City or Manila in the Philippines, to Singapore, to Bali Indonesia, back to Bangkok. Which would be a great smorgasbord of all that the region offers; if you could get that as a 5 to 10 stop package I think you would have a real winner for Asia visitors.