Journals

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Reason 1: Isaac has a better arsenal of gadgets etc. (he can fly or throw exploding tears)
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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)
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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.
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Honorable mentions:
Better modding community than half life's:
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Better character design (hdtf and blue shift are an exception):
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(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...