The Tomcat and the Hornet were designed for rather different mission profiles, so to compare them is not really fair.
The Tomcat was designed to fit a requsition to replace the F-4 Phantom IIs as fleet air interceptors, with emphasis on the beyond visual range interception role, hence the Tomcat could carry the ultra long range Phoenix missile and its related operating systems. While the Tomcat can dogfight, it was not initialy intended that it would let threat aircraft get close enough to it to make the dogfight situation likely.
The Hornet, by contrast, fits into a category of combat aircraft usually refered to as multi role combat aircraft. The idea of the the MRCA came about in the 1970s when the economics of specialist mission aircraft (such as the Tomcat) were being questioned. The question was, why build two different airframes, one for air to air combat and one for surface attack missions, when you could build one airframe that could addapt to both? In other words, why shoot money at two aircraft when you can get one aircraft to do it all?
The Tomcat is a mission specific aircraft, specific to the interceptor role. The Hornet is an MRCA, beyond calling it a fighter, its not terribly specific about what mission profiles it takes on in the air combat arena.
To compare them is like comparing a meat cleaver to Swiss Army Knife: One is designed to do one job very well to the exclusion of others, the other is designed to addapt to almost anything you can throw at it without losing a beat.
As for my favorite between them: I like the design of the Hornet in the A through D versions, but I dont like the E and F much.
The Tomcat is a beauty no matter what version you’re looking at.
If you’re in battle and aren’t sure what you’re up against, load up a Hornet and hope for the best.
I you see something nasty coming in by air from a long way out and need to knock it down, get in your Tomcat and ride!