These delays are not because there are major problems. What happens is this... the cycle for a new, specific, individual technology to become molded into an operational form (a new black box), THEN integrated into a system like the F-35, can be lengthy.
In WW2, you simply added whatever item you wanted to an airframe. Today, everything in a jet is integrated, and a new capability can't simply be bolted on.
Let's say DOD scientists say "We have this really cool device that can spoof an IRST system." The word makes its way up to those in power. They investigate. "We MUST have this on the F-35!!" The F-35 engineers now need to help develop, install, and test the device or capability into an airframe that is highly integrated, with all components communicating with each other. The new system affects all the other systems on the software bus. Compatibilities must be checked. While this is going on, ANOTHER "must have" capability is developed. The procedure repeats. Budgets get rehashed and trashed.
But what comes out at the other end is a superior product. If the PAK-FA is rushed, it will not reach its potential.
The same thing happened to the F-22. Expected IOC was pushed back, and back. If it was forced, and deployed in 1996, it would be substandard to what we have today.
In this day and age, systems are designed in a highly modular way.
it doesn't matter how new or how old a particular added subsystem/functionality is, its input and its output to the system is known. The "software bus" is in actual fact a hardware/software communications channel, with known protocols, timings, sychronicities and controllers. All subsystems communicate in a certain way, known and established, when they are developed is irrelevant as long as the main structure is solid. To give you an example, it doesn't matter when you connect a very powerful PC to the network, what matters is that the network is there, the comms protocols are the same for all computers in the network.
I believe it is not integration problems that are holding back the F35.
I think it is the actual plane not meeting its original design specifications in a number of areas.