Is bus the best option?
Depends on your preferences, because if you have plenty of time and want to travel cheap, then probably bus is your best option. But if you have limited time and ok paying a bit more for the journey, then you can always fly (e.g. Kayseri-Denizli via Istanbul with Pegasus Airlines or Turkish Airlines)
Will we need to book in advance?
It is not just one bus company running between Cappadocia and Denizli (Metro Turizm, Suha Turizm etc.), so buying in advance isn't a necessary measure.
Is there anywhere midway to stop over for the night?
If you look purely geographically, then obvious choice here is Konya, it is roughly half way between your destinations + historic and relatively interesting place. But in case you prefer seaside stop, then you can always take a minor detour and make a stopover somewhere around Antalya
Is it possible to do the trip by train?
Yes, you can travel by train, but it will be very time consuming, since you have to travel first from Kayseri to Ankara (roughly 7 hours), then board Ankara-Izmir overnight train and get off in the morning at Alasehir, which is roughly 90 km from Pamukkale
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