Your article is old, basically. In 2005 American Airlines was operating over 350 MD-80s, this year that will drop below 200 and they will be gone all together in a few more years. The current generation 737-800 is about 20% more fuel efficient than an MD-80 and carries an extra 10 people (in current configuration, was 20 more). They are also retiring the 757s and replacing with 737s/A320s/787 all which are much more efficient.
Airlines did not invest in fleet replacements from 2001 to about 2009. American had been taking 737s to replace older aircraft, but suspending the fleet replacement after 9/11.
There was a large dip in new aircraft designs during the 90s/early 2000s as well. Basically Boeing gave us the 737NG which was an improvement over the classic, but not earth shattering and the 777 which was a massive improvement over the 747. Airbus gave the A330, which was about the same as a 767, and the A340, which is a dog.
The 787 gets 20% improvement over the 767, 737Max and A320NEO will get a 12-15% increase over current gen aircraft. The A350 will get 20% better than the A330 (IIRC) and the 777Max will get 10-15% over the current 777s.
Also I am not sure about your source, seems that an agency pushing for cap and trade on airlines is probably manipulating the data to help their cause. Such as looking at every fleet at their max range, which is a very small percentage of flying and hides a lot of the efficiency gains, since efficiency gains can be traded for longer range. It also completely hides operational changes than have reduced fuel consumption, like using ground power/air at gates instead of APUs, single engine taxis and use of high speed tugs. It ignores engine cleanings, etc.
Here is an ATA article from 2009
Link
As for passenger traffic, in revenue seat miles, we are basically at the same level as 2007, and has been climbing since 2009. Here is a
link you can play with, pretty cool site.