I think it depends a lot on what you can afford and are willing to pay and also on whether or not you have a vehicle.
For me personally, as I live in Plymouth and am travelling on foot this year, it makes sense to go from Plymouth rather than Portsmouth. The fare for a foot passenger is probably less than the train far to Portsmouth and back plus a ferry ticket.
There's also the advantage that, on the return trip, I'll be hot, tired, sweaty and aching and I'll still be able to step off the ferry and be home in ten minutes by cab, rather than facing a long train journey with all my kit to carry.
Although I do agree that Brittany Ferries are probably the most expensive ferry tickets to France, especially when compared to LD Lines or Transmanche.