I agree, things need to be standardized (sets, lives, difficulties, etc.) so nobody's playing an easier or harder game than the rest of us.
That being said -- my observations so far:
- on Arcade/MAME, nothing beats the red gun. It takes out the smaller ships that can be annoying very fast.
- on Genesis, the blue gun is surprisingly effective.
Keep in mind, Genesis version is easier -- not only is there a dedicated rapid-fire button on C, the bomb on that port clears the entire screen, compared to the arcade bomb which is a smaller radius from where your ship was. Also, less enemies/annoying mid-stage ship groups. Plus, difficulty overall is much easier based on settings I'm using.
My settings:
MAME
Difficulty - Medium (default)
Lives - 3 (default)
Extra Lives - 70K/270K/200K+ (default)

Best score, a paltry 83,830 & Area 31. Having trouble with those green mid-level ships that fire straight down when you're underneath them, and regular shots when you are not directly under them. Not liking the total slow/pea shooter checkpoint restarts, but hey, it's the nature of the SHMUP, right?
Genesis (Fusion emu)
Difficulty - Normal (not half as difficult as the arcade)

A better score -- no continues were used either -- 175,700.
Ultimately, it is up to the community on a standard we should all be playing Truxton on, but I feel the defaults are best. I've challenged myself to stop wimping out on difficulty, and I know these scores will be easier to beat with a little pattern practice.