Tetris deserves to be somewhere in the top twenty, or at least the top forty. It’s literally a near perfect game in that there’s not much you could do to improve it’s flawless design. Adding more complex mechanics, or a story would only serve as gimmicks on top of it’s intrinsicly rewarding feedback loop. Although if you want a (dark) story for it you could say it mirrors the struggle of life. In it’s circularity it also has something in common with Citizen Kane, a film that is often placed at the top of greatest films of all time lists.
Should all games strive to be as minimal and complete as Tetris? No. We benefit from a range of different games, some on the pure game end of the spectrum, others on the hybrid, moving towards film end. I think Polygon’s list favours the pure game approach, featuring lots of Nintendo games that put gameplay first and foremost, often neglecting things like story. That could be why Orta is on this list but not Saga - as a pure game it’s mechanics are the more direct and involving of the two.
Where Panzer Dragoon Saga excels is in its hybrid nature. As @Shadow inferred, it is not great at just one thing, but a wide range of aspects. Gameplay, art, visuals (for the time), world building, story, audio, knowing what to leave in and leave out. All masterfully done. It’s not a perfect game and for most of aspects you could find technically better examples in other games, especially as a pure game with it’s random encounters and mostly empty maps. Yet when looked at as a whole experience it’s unthinkable that it didn’t even make the top 500.