well, this is all just my opinion, but I will try to support it with some facts.
First, the Super Bug is a more versatile platform. The Strike Eagle is designed for air to mud, but can still fight in the air. The Hornet can fight in the air, drop bombs, conduct air-to-air refueling, drop leaflets, fly photo-recon missions, and now with the new EA-18 variant, it can also fly electronic warfare missions too. Hands down, the Super Bug wins versatility.
Someone mentioned engines. This is really not a good indicator of anything. The Eagle has more powerful engines, but it also has a max takeoff weight of 15,000 pounds more than the Hornet. Of course, the F-15E has a higher top speed, but that is seldom used in today's combat.
The radar and electronics are generally better in the 18. This is only because the Strike Eagle is an older plane than the Super Bug is. The upcoming radar refit for the Strike Eagles is to use the same radar as on the F-18F. But at least for now, the -18 has the edge here.
The Strike Eagle has a fly-by-wire system, but it works WITH the hydraulic control system. The Hornet has replaced the old hydraulic system entirely with fly by wire quaduple redundant computers.
Strike Eagle definitely has better range as well. But remember, these are not comparable planes. The Hornet is a multi-role fleet aircraft. The Strike Eagle was designed for one mission--the deep-penetrate strike. This is the role that the F-111 used to fill.