While Homura is more skilled fighter here, Natsu isn't a pushover either. He fought a
trained assassins dark mage,
someone who can literally hear his mind,
a dark guild Master, and
this motherf***er.
Natsu resistance to fire obviously giving him an edge here, basically making her fire manip useless. Telekinesis? Natsu deals with it on Daily basis in form of Erza. Stats amps? Natsu can boosts his power drastically when he pissed.
Homura can hurts him by punches, kicks, and slashes. But she has to deal with Natsu DS Magic in order to do that. She can try stealth, but Natsu enhanced smell and hearing can counter that.
Overall, I will give this to Natsu Mid-diff. Homura slight superior skills can only delayed the inevitable before Natsu beat her via spamming long range attacks.