In my opinion? They're way, way too different to choose a "favorite." And this is coming from a hardcore fan of the original, who didn't play 64 nearly as much.
To be honest, though, I definitely prefer the overall feel of 64 more. The original SNES version was kind of a downer. 64 was more kiddy, but if I could go back in time and give my eight-year-old self the 64 version to play instead, I'd do it. I think that's why there's much more support for the 64 version than the original here: the SNES version rubbed most people the wrong way, but the 64 version was so campy, bubbly, and colorful, you couldn't help but feel good during play and afterwards. So, my theory is that the preference for the 64 version is based on the difference in emotional weight between the two games. The original game was darker and moodier than the sequel.
Observations about subtle differences between the two to support my point:
- The vast majority of music in the original was in the minor key, and had heavy military undertones/themes. I don't remember the 64 music quite as well, but I remember the music being more chirpy and upbeat.
- The sound effects in the original were harsher. The sound of your Arwing taking heavy damage was this insane crunching noise. I'd always feel TERRIBLE when I heard that as a young kid, and I'd be traumatized for a second or two. Hell, even now. And the music and sound effects when you died made it feel like a grave thing had just happened. Contrast this stuff to 64's effects: softer, less grave. As I recall, the music when you die can aptly be described as silly. Basically: "no big deal, try again, kid! *thumbs up*"
- The focus on dodging things in the original was brought up in the OP. Good point, but it supports my theory. This really adds to the challenge of the game, and makes you feel vulnerable at all times.
- The voices in the original version are these weird bassy gibberish noises. In 64, your squad's voices are higher-pitched, they talk to you more often, and they actually speak English. Your squad basically keeps you company throughout your mission.
- A number of the bosses in 64 talk to you and taunt you. In the original, you're fighting these silent, bizarre bosses. Unknowable alien weirdos.
- Art-wise, the original was dark and gloomy, on the whole. The 64 version was bright and colorful.
And so on. I'm sure I could think of more examples if I tried. My point is that the original was heavier on people. 64 was light and fun. I played the everliving crap out of the original when I was little, the polygons were absolutely amazing to me back then (I'd never seen anything like that), the music WAS cool (I actually now remember my first five minutes or so of playing, with my family around me, me making comments about how mindblowing it was ... sniff). But, to be perfectly honest, months after that, I don't know if I'd call most of that time "fun." I was basically on edge the whole time while playing. And whenever I'd finish a playthrough, I'd think, "Man, I don't feel so good. That was kind of a bummer."
I envy the younger kids, the 64 generation, who experienced SF64 first.