I would say St Pancras, if arriving by train from the continent its where you arrive. Externally the frontage is really the Hotel, but no less impressive, and for someone of my age who travelled through it a few times to Sheffield in the early 80s it was a dingy nasty place, the transformation is one of the success stories in recycling a Victorian structure and making it fit for the 21st Century Equally Kings Cross next door has undergone an similar upgrade and is a much nicer place than it was in the 70s and 80s, and clearing the area in front of the station and adding the modern extension at the side works well. Paddington would then be No. 3 on my list for London
Looking outside London: York would have to feature, with most of the original 1877 station surviving, albeit with some major repairs over the years particularly after WW2. Its position as a major junction on the ECML and its association with the National Railway Museum means it is important both in terms of rail travel and rail history. The only slight negative is that having the road and bus stops right outside means that its difficult to get an unobstucted view of the frontage.
There are lots of other interesting stations, but these wouldn't qualify as flagship, e.g. Manchester Oxford Road for its use of laminated timber, Canary Wharf, some small stations that have remained as is since they were built.