Nihilus is gangsta foo. Since this all comes down to Ganon and Nihilus I'll only count their stats.
Strength: Ganon sends normal sized human beings flying with one arm and is one of the few people taller than Nihilus(just like pointing that out).
Speed: Nihilus is a Sith Lord and thus can increase his speed with the Force but I'm not sure by how much. Ganon is also very fast despite his size and can teleport, so I'll say Ganon(if anyone knows sumthin about Nihilus' speed I don't tell me).
Durability: Ganon, with ease. Guy survived a giant dragon breathing fire on him and his whole fortress collapsing and lived.
Melee range: Ganon wields large claymore-like swords as big as normal people one handed.
Range of powers: Ganon has different types of ranged energy balls, can cause shockwaves with punche that go about 40-50 feet around him, among other things, Nihilus has drain life, force lightning and I think force choke, so it's a tie.
Power:Ganon's powers are on the whole more destructive and forceful than Nihilus', with the exception of Force Killer, so I'll say Ganon. It's close tho, as Nihilus does have powerful enough TK to lift his whole ship and possibly his fleet, and keeps the ship together.
Versatility: Ganon has much more different powers than what Nihilus has shown, like teleportation, pulling opponents into different dimensions, causing shockwaves with punches, transforming, increasing speed or strength with ToP, and possibly even creation of living creatures like Phantom Ganon.
Experience: Ganon is thousands of years old, he's seen and done much more than Nihilus.
Skill with weapons: Ganon is a master swordsman and has been shown using both single and dual bladed styles,Nihilus' saber style holds the lightsaber in one hand while he uses force attacks with the other, so I say tie.
Intelligence: Ganon is a master manipulator and is extremely intelligent, whereas Nihilus, tho not stupid, can be tricked because every action he makes is to satisfy his hunger.
Coolness and badassry: Tho Nihilus is very cool and badass, I say Ganon.
Overall, Ganon wins after a very hard fight.