Well, in the mid 50's/early 60's the jet aircraft was the new airplane style and an inovation.
By the early 1970's size was the inovation (the increase in capacity from 707 to 747).
The 80's inovation was range. 747s/767ERs/L1011-500/etc.
The 90's inovation is the regional jet.
Somewhere in there also fits the Concorde, a speed inovation; however, it was not a blazing success. How can anyone call 14 Concordes flying at peak time a success? Yes it flew, yes it is fast, yes it was a new design, but it was unique. And no other airlines wanted them...
Who knows what the 2000-2010's inovation will be. Will it be size? (A380) or new design/speed combo? (Boeings' Sonic Cruiser).
The A380 has the orders, a firm launch, a possible service entry date, a design that has been tested on computers/wind tunnel/etc. The A380 looks like a reality.
Boeings' Sonic Cruiser (BSC) has no orders, a sketchy design, no real service entry date, and was just recently announced. But BSC has peaked an interest in airlines. If Boeing can keep the costs to buy and operate the BSC within the range of current aircraft types it has the possibility of being a huge success. If it is costly to operate and inefficient, then it will just be another Concorde--a unique but highly unprofitable design.
So to answer the question, it may or may not be the inovation of the 00's.