I've horse whipped both the 5.4 and 6.2 Raptor. Some things I agree with Birds opening post...
Immediate off the line power is pretty similar between the two. The smaller displacement 5.4's larger stroke does a good job producing torque off idle. Even though (as far as I know) Ford has still yet to publish a dyno graph for the Raptor 6.2 engine, I believe the difference in torque curves between the two (to 2500ish rpm) is very minor. I say its a draw between the two (up to 2500ish rpm), and give lack of traction the win.
Both the 5.4 and 6.2 shift like shit. I drive a lot of different cars every year (roughly 1000-1400 depending on how busy the years been [ I keep an excel spread sheet for almost every car I service, so this is easy to count]). Unless the vehicle actually has a transmission issue, I can't remember any that shifts as ****** as the later F150's. The 6.2 does feel less labored when pulling hills, in sand, or mud, so the transmission does perform slightly better over the 5.4. But around town they both; down shift hard erratically when coming to a stop, hunt around/gear surf when pulling long hills, and have extreme hesitant passing gear engagements. I give the 6.2 the slight edge on shifting only because it feels less labored, but overall I think Ford gets the big fail in the shifting department.
The 5.4 appears to get better fuel mileage, although I don't think by much. They both hog gas when you're pushing 6000lbs on 35's with kite like aerodynamics. MPG... 5.4.
Can't comment on towing between the two.
Where the 6.2 out performs the 5.4: Anytime you're leaning on it above 3000 rpm. The 5.4 just runs out of steam. (It also doesn't help that I live 6700 feet above sea level which takes its toll on engine power). The physical characteristics of the 5.4 limits its upper power band, it always has. Untill the 6.2 came along, every other light duty truck manufacture engine was driving circles around the 5.4. The 5.4 has bottom end, but thats about all. The 6.2 fills the gap by producing a solid, uniform power band from idle to red line. The power needed when exiting a corner at 3500 rpm in deep sand, with over sized heavy tires, power when needed to pass a line of cars and carry you through at 5000 rpm. If you can't feel the difference than I just don't know what to say.
There's a whole nother' reason why I bought the 6.2 over the 5.4, and that's potential, but since I don't think we're going there (yet??), I'll skip it.
There was a time I really enjoyed getting knee deep in the 5.4 vs 6.2 arguments, not so much anymore. Both 5.4 and 6.2 Raptor owners have been enjoy their trucks for their own reasons. What works for one doesn't work for all. If the 5.4 is working for you, then great! I respect that, just in return respect that the 6.2 works for me for my reasons. As for the debate about which ones faster, and Irons video, and shit not adding up on paper and bla bla bla, I don't care, I'm happy with my 6.2.