Johor Bahru is the state capital of the state of Johor and the second largest metropolitan area in Malaysia. Most tourists don't stop here and just pass through the city on their way to or out of Singapore. JB is a major local transportation hub however. Since it is just across the causeway from Singapore, some travellers use it as a hub to visit Singapore from here (lower accommodation prices) or to board the train, bus or airplane.
Kuantan is the largest city of the East Coast of Peninsular Malaysia with a population of about half a million. It is also the capital of the state of Pahang.
Kuantan is located about halfway between Singapore (to the south) and Kota Bahru (to the north). The city is situated at the coast of the South China Sea near the mouth of the Kuantan River. The city is not a major tourist destination, rather a stopover point for island destinations (Tioman, Redang, Perhentians, etc.) along the East Coast. From Kuantan you can also also reach the popular beach in Cherating in less than an hour with the local Bus.