A couple of points that need to be made:
1. Since the introduction of the 747 in the sixties, only one major aircraft program (the 777) has been completed on time. Why? Because building a brand new aircraft from scratch is far more difficult then it seems.
2. Why was the 777 on time? Because Boeing spent a ton of money and program managed it to death. In retrospect perhaps they should have done the same thing with the 787 program.
3. The current process of building major airplanes is to design the prototype/test aircraft, begin building them, fly them all the while continuing to push aircraft down the assembly line. While the test program is being carried out, the production line and off-line production aircraft have the modifications completed based on the results of the test program. The idea behind this is that it is generally faster, however in practice is becomes a logistical nightmare trying to upgrade each individual airframe with the required modifications to meet the final certification requirements.
4. This is a problem that plagues all the major aircraft manufacturers - Boeing, Airbus and Bombardier. No one is immune. It is one of the reasons why aircraft manufacturers prefer to modify existing platforms by putting in longer range fuel tanks, a plug in the fuselage to provide 20 more seats, new wing designs, etc. It is a lot faster and cheaper than designing, building, and certifying a new aircraft from scratch.
5. If you own/run an airline, NEVER, EVER, BE THE FIRST CUSTOMER. Ask SAS about the Dash 8 Q400, Singapore Airlines about the first A380, and now ANA about the 787. If you buy a completely new aircraft design be prepared for it to be between two and four years LATE to the original promised delivery date.
6. I have toured both the cabin mockups for the 787 and the A380 and they were both awesome compared to what is currently offered. If I was lucky enough to be offered a maiden flight I would jump at the opportunity.