I enjoy and respect both series, it's sadly hard for me to pick favorites on them.
That and I must not be very active in the SHMUP community, I've never seen anyone rave over any types of Shmups.

Though I do have respect for Gradius being a very, VERY classic series that seems like it set a very solid image for the SHMUP scene to follow and build on.
Shame Sony told Konami nope and making a gradius for ps3, and then fucking konami just
konami'd

After Konami released treasure's Gradius V on PS2, apparently while it may be regarded as the best Gradius game
(Treasure made it, of course it would be the best. They made Radiant Silvergun and Ikaruga, which silvergun is usually regarded as the best SHMUP to exist, least as I've seen.)
But I guess it didn't sell too well. So when Konami wanted to make a Gradius for Playstation 3, Sony said nope, don't even try, nobody will buy it. So it kinda just ended there.
And now there's not even a chance of Konami releasing another Gradius because they're less concerned about Gradius at all, AND NOW they're even less concerned about good video games.

And to add to your Shmup stuff, It's always kinda just been like, Gradius 5, R-Type finale, Radiant Silvergun and DariusburstCS that's like, my top SHMUP boys. Hard for me to decide which is my total favorite because I go through moods.