Pyramidion is just very elegantly made, simple to crew and pretty straight-forward to fly. It's very easy to engineer on pyra, because all components are very close together, in good places. Engineering on any other ship is significantly harder. Also, as only ship it has a small, protected baloon, which makes charging with it less risky.
For instance engineering on junker has few problems:
a) long distance from front to back of the ship
b) long way from bottom deck to upper deck
c) ladders which have to be used all the time (for instance in pyramidion it's not a problem because you go on ladder once and that's pretty much it)
d) division of duties on the ship is not obvious (many times I see engineers staying downdeck, and many people do not realise they can hit the hull from the front part of the ship, I think in english it's called the nose?)
I think those kind of things may have not been thought through/playetested enough, so pyramidion has constant advantage of elegant, inteligent design. Combined with effectiveness of combos consisted of two light guns it makes it a great ship to fly and crew.