Saturn, Dreamcast & PS2 with, by extension, PS1. PS1 after all has some great titles like Zanac NEO, Raiden DX (plus Raiden Project), Delta and Gradius Gaiden no to mention, many shared titles with the Saturns shmup library (Konami collections, AGears titles etc). It has better ports of the Donpachi titles too.
Anyway, all said and done, I think I enjoy my DC shmups the most. I'm not going to cite the old quantity > quality, as it's not true. But, I love a lot of the titles for DC, especially Mars Matrix, GigaWing, Zero Gunner 2, BDown and Under Defeat. Not to mention, Ikaruga. I even like the average ones like Chaos Field (quite unique) and Trizeal (falling medal system!) too. Also, the DC is where I learned to appreciate and fall in love with the shoot em up, so that definitely is a factor too. Saturn importing came later for me (mid 2000's).
Ironically, Battle Garegga on Saturn is my fave shoot em up, closely followed by Mars Matrix...