I've done both Santander and Bilbao- Bilbao rather more frequently (because it is a mini cruise in terms of the length of crossing).
At Santander you arrive right in the heart of the city- which is great if taking bus or train (main line or the Coastal narrow gauge) onwards, or to explore a city which I like a lot.
In my experience you are more likely to get wildlife sightings on the Bilbao route. But you arrive in an industrial port somewhat north of the city, there is a not very convenient hourly bus into the city, but it's overall a lot worse location than when they docked in Santurtzi. At least from Santurtzi there was the metro train into the city.
If driving then at Bilbao I think you are straight out onto the motorway network.
So very much swings and roundabouts.
I'm a great fan of the French atmosphere and service on all Brittany Ferries ships.
In terms of the ships think of the Baltic sea routes (such as Sweden to Finland) in terms of quality- almost cruise ship standard. For quality/experience I don't think North America has anything like them- not even BC Ferries. I've not been on any of the long routes in the Maritimes, so can't compare those.
Plymouth Millbay Docks to me is a bit of a basic or functional port, especially for foot passengers.
Portsmouth is way more convenient to its city (even National Express buses stop there) and a very nice port building, more a sense of occasion. It replaced a more basic period piece terminal- that was good in its way but the new one is far better. All ferries and cruises at Portsmouth use shuttle buses ship to/from terminal building.
Regarding the step into the bathroom and shower I'm pretty sure that you have that, I believe (possibly erroneously) that it is maritime law, to guard against flooding of the main part of the cabin in rough weather.
As a foot passenger I therefore prefer the Santander route. If the Bilbao port was closer in it would be a very tight contest, too tight to call.