Yup there will be a few options at the start ( meaning you can either skip prologue , skip to Day 2 , skip to end of Version 0.2 )
But from 0.3 content onwards since the :
Karma progression ( Personality [ Good to Evil ) &
Route Progression ( Decisions made on World Affairs )
are applicable the skip option will be disabled from that point of content
Also certain hidden collectibles and conditions will sadly be lost if you decide to directly skip but I've made it so that it doesn't affect anything too badly later on.