My 04 does it to. Seems to be normal. A guy i work with just bought a 04 just like mine and his does it to. As it gets some miles on it it will get better but every once in awile it will still do it.
I got mine with 8 miles on it an it now has 17k on it but every so often it'll do exactly what you said.
Even though you had the same engine before the newer ecu's seem to play a huge role with how these engines respond. Somne people have said there titans do it to on occasion and its the torque management kicking in.
The titans make tons more power than our 4 cyl frontiers but i think its the same system on the frontier but i dont know why we would need it.
Our trucks are set up to get optimum fuel efficiency so the ecu seems to always be in a lean mode. When i hook my trailer up to my truck with 2 atvs on it, it seems to wake it up despite the extra weight.
These ecus are really sensitive and it does a good job towing especially for a 4 banger.
Unhook the trailer and it accelerates briskly for the rest of the day until the ecu realizes the load is a lot less and goes back in to the fuel saving mode.
Hope this helps