It's not one reason but all of the reasons posted here basically and a few more:
-He-Man is more 80s than the turtles and a much harder franchise to make "cool" again.
-It aired on Cartoon Network as opposed to SatAM over the air (2k3 also failed on CN)
-4Kids had a lot of money thanks to Pokemon/anime so they could spend money on 2k3 even if it didn't make as much money.
-4Kids needed shows to fill up their kids programming block they had (FoxBox/4KidsTV) so 2k3 was an easily renewable show
-They messed up the toys by releasing figures no one wanted
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