You have to make a choice after the prologue mission and the intro cutscene for three stat bonuses from two weapons and one Guardian Spirit.
These stat bonuses ARE PERMANENT! A Book of Reincarnation will only give you back all spent amrita but these initial choice IS EXCLUDED! Important for the min/maxers.
The weapons you can choose state their corresponding stats:
Sword - heart +1
Dual Swords - skill +1
Spear - body +1
Axe - stamina +1
Kusarigama - dexterity +1
So do the Guardian Spirits:
Kato (wolf) - strength +1
Isonade (water/shark) - spirit +1
Daiba-Washi (wind/bird) - skill +1
After your choice you are presented on the right hand side with attribute bonuses according to your chosen weapons and spirit.
Considering that most builds will probably be using their spirit guardian passives (at least 12 spirit), Body for hitpoints and Heart for Ki I think they way to roll with these lilttle permanent bonuses would be
Sword - Heart +1 (Ki)
Spear - Body +1(HP)
Isonade - Spirit +1