My father has the same truck you have, 06 f150 xcab short bed 4x4 5.4 triton.
His truck is very nice for a half ton, but comparing the half ton market to a 3/4 or 1 ton is apples to oranges. I believe my truck gets better fuel mileage his 5.4 v8, I also feel that his truck feels underpowered, maybe thats cause I drive a cummins. What do you get with the 06 early 07. You get a proven motor, you get 325 horsepower and 610 foot pounds torque. You will notice with true diesels, a healthy diesel will usually make close to double the torque as the hp numbers. Part of what fuel efficiency the truck has is due to the high torque numbers. your looking at 231hp 293 tq with the smaller v8 and with the 5.4 300/365 with the larger. So off the bat you get more power. I dont know if you tow much, I dont, but when i do I have the power to do so safely. Speaking of safely, If you have something you need the extra power to pull, its probably pretty safe to say the heavier duty chassis is a def bonus.
the 24v 5.9 in the 06 and early 07 is the last model years before the 6.7. This was the last models of the 5.9 where its still considered non modernized, epa untouched, and as the years get older they become less restricted. AS stated earlier, we have an in cylinder egr system, but thats about it and Ive never heard of, or dont recall any issues with that. As stated previously as well, EFI is available for the 06 early 07. Its the top of the line tuning system. The motor can handle a heck of a lot. Dont let people run you off because of the transmissions. In stock form the transmissions are pretty solid, its when you start throwing more power at it then its capable of handling you run into problems......fast. No one has really ever given exact numbers, but I recall being told years ago with my first 06, anything over 75 extra hp on my new at the time truck and tranny would be asking for trouble with the stock tranny. If you tune the motor, just behave and dont dog the tranny and youll be good for a while.
What are you getting? your getting cummins reliability cummins power and cummins dependability. One thing you notice going on vehicle forums, more people come on and post threads about issues they are having to receive help. It gives the appearance that there are more issues then there really are. You have your enthusiasts who build monster power, so yes, of course they will have their issues, but again, youll find the family of cummins owners very helpful so many people ask for help before going to shops or dealerships, again, dont let that scare you. Ive owned 3 diesels, 2 cummins and 1 powerstroke. Ill never own another powerstroke. I love my cummins. Take care of it, and it will take care of you.