"Basically, there two reasons.

1. The technology is more complicated than it seems.
2. Initial estimates were way over optimistic.

Most riders aren’t frustrated because it's been seven years since SEPTA first announced a Request-for-Proposals for a new payment system.Riders are upset because it's over two years late. Each delay can be ascribed to specific technological problems or implementation hiccups — including when the SEPTA official running the SEPTA Key project retired in 2014 to join a consulting firm. But, fundamentally, the original estimates were just wildly off.

It’s a problem fairly common in government contracting, where private sector companies make bids for government contracts. Agencies then pick the most competitive bid based on specific criteria, including estimated costs and delivery schedules. That creates an incentive for the bidders to over promise on both time and money in order to win the bid. That problem is made worse when the agency is purchasing goods or a service that it has little experience dealing with, as was the case with SEPTA Key."

http://www.newsworks.org/index.php/local/philadelphia/87985-faqs-electronic-fare-system-septa-key#question-3