- He has more experience (he has seen more battles and war)
- His attacks are very difficult to read
- He has full control over his Bijuu
- He's a master swordsman
- He is very tough(he can take damage)
- He has an edge against Genjutsu(because he's a perfect jinchuuriki)
- He seems very proficient with lightning
- He is faster
- He mastered Senjutsu(which grants various things like strength, speed, sensory abilities, healing, Ma & Pa's help etc)
- He can sense malice
- He is quite proficient in taijutsu
- Frog summons(almost forgot this)
If Bee is stronger than Naruto then it would be because Bee established true control over his bijuu and because he has more experience.
If Naruto could combine SM and KB mode he'd definitely be stronger than Kirabi.
FINALY SOME1 Who understand thats what i mean lol but Ma & Pa cant connect with naruto and actaly bee tough him KB mode