When talking about "the end of FF programs" you have to be more specific. Upgrades during non-peak times, priority security, priority boarding these are things that will never go away because they have virtually zero cost.

But what is likely to happen?
1) A reduction in first class and business class award seats. As airlines get better at nearing 100% occupancy on planes I expect first class to nearly disappear and business class to reduce in size in order to add more economy class seats. If there is an average of 4 paid bus class per flight expect those 12 chairs to be reduced to 4 and for 21 new economy class chairs to be placed in their wake.

2) A devaluation of airlines miles. Airlines will still make all their money by selling miles to credit cards and "having a frequent flyer program" but we will see what Delta is doing right now expand to other carriers. The days of 20,000 miles getting you a flight will go away and it will cost more like 40,000 for an economy seat. This won't happen at once, it will be a measured set up 20% increases over 4-5 years. See: Hotel loyalty program devaluations in 2012 and 2013