Reason 1: Isaac has a better arsenal of gadgets etc. (he can fly or throw exploding tears)
Can make deals with the angel and the devil also...
Reason 2: God can intervein events for his favor and Isaac can call powerful allies to his fights.
Reason 3: Isaac is more endurable (physically and psychologically).Isaac takes no damage from falling and can survive explosions and such.
Reason 4:
Eden. No elaborating words... too self-explanatory. (Wsaac)
Reason 5: Isaac can come in many versions.(Lazarus for example)
Reason 6: W ending . In this reason, Isaac proves hisself to be more real than Half life characters.
Honorable mentions:
Better modding community than half life's:
Better character design (hdtf and blue shift are an exception):
(too f#cking cute!!)
(when you compare him to Gordon Freeman and Adrian Shephard you can see how dull they are)
You can see how mighty Isaac is after reading this...