With the royal palace in the CBD, it's only natural that they would not want its surrounding areas to become a ghost town. It is just not possible. Looking at the the locations of the US White House and our Istana are good live examples.
With the MRT coming to JB and their eventual LRT linkup to Kempas, the new upcoming EDL and the widening of the roads around Danga Bay and the Lido Beach and the proposed large shopping mall at Jalan Bakar Batu (presently a military camp), the upcoming hospital by Peter Lim and the Sultan in Stulang, all of which will bring about more life into the area. I don't think they will want to waste all that money spent by not including the upgrading in the CBD. However, all these will take time and may not be as fast as what is happening in the Bukit Indah area today.
I have already seen several of the old houses in the Taman Pelangi area being bought by new owners and renovated extensively and tastefully. The only disadvantage is that these old Tamans are not gated and guarded. These areas are slowly but surely picking up. People are already foreseeing the advantage and benefits from the future MRT connection. It just doesn't make sense for the state government to build such a grand CIQ at JB and then leaving its surrounding area as a ghost town eventually.
Overall, there is presently too many shopping malls in Johor Bahru, but not enough people to sustain them. Just visit any of these malls on weekdays and you'll know what I mean. To enable Johor Bahru to be commercially successful, they will need to attract more people, either to live in JB or more visitors from Singapore. The launching of JPO, Legoland and other attractions are just what is needed, and more. Ironically, when this place will get too crowded by then, it becomes no better than living in Singapore anymore in the future. Sigh....