Well if we look at high speed rail prices around the World they could be anything from £10 to £150 one way, varying from advance to anytime single.
Like anything, it will be priced to fill the trains at the most cost effective manner. Nothing running round empty is helpful, so you change your pricing strategy to balance people wanting speed v cost.
This sort of situation already exists in the UK, I can get from my current home to my parents home. Leeds to Wigan using Transpennine, change at Manchester and get a TP train to Wigan via Chat Moss (well i could, might have changed now Bolton is electrified) or get the Northern all stops direct to Wigan (via Halifax, Victoria, Wallgate onto Southport). Option A is over twice the cost of option B but is a lot quicker. Option B makes its money on all the shorter intermediate journeys.
If you are going to add a whole new railway for capacity, might as well make it a quick one.