First, a summary post; I was going to dig back for specific Frank quotes, but it's too much work.
On Newton and Seven:
Since this is a mysto-magical grenre, seven being a mysto-magical number that Newton liked is the best reason to have seven colors.
More than that, Newton used the words Blue and Indigo, but what he meant was:
Blue-the-color-of-the-sky (the part at the top):


and not

which has a bit of a violet hue and so is called "Indigo" today.
Now, it depends a lot on how you render the spectrum on your monitor, but when I look at the spectrum:

I do see six stripes. Violet, Blue, Cyan, Green, Yellow, and Red. So if we were going to go six colors, the color I'd drop would be Orange. Adding brown (which is, in fact, dark orange):
RGB = (128, 064, 000) for Brown
RGB = (255, 128, 0) for Orange
why doesn't bb-code recognize that as a URL? Do I need to escape the )(s or something?
Just doubles down on the crazy. Now, if you want to have Brown instead of Orange, and make red a brighter red - yeah, that would improve contrast.
So:
(Bright) Red, (Dark) Brown, (Bright) Yellow, (Dark) Green, (Bright) Cyan, (Dark) BlueIndigo, (Bright) Purple/Violet
would work fine since Violet and Red are pretty easy to distinguish even if they are both bright colors.
Blackwatch Plaid
On having something like WH40K or Shadowfist and not a color wheel at all:
It is absolutely true that you are enemies with your opponents deck. Wing Commander and Netrunner both failed critically on this point.
So, red decks have to be able to play against other red decks, that's a given.
But at that rate, what Frank is really saying is: why have a color wheel at all? Why not just have a bunch of factions and all animosity table, like Shadowfist or WH40K?
To which I say: the purpose of having a color wheel, instead of some arbitrary animosity table, is the shared enemies pattern. So Blue and Green are allies because they both hate Brown, that sort of thing. In order for this to work, you need an odd number of colors.
This has all sorts of advantages. When Brown is ascendant, Green and BlueCyan are buddies and Yellow and Indigo have to take a backseat. So shared enemies automatically give you shifting alliances, which is good.
Blackwatch Plaid
So, wait, are you still saying more colors isn't harder?
So Frank did a reasonable job setting up six factions, but that doesn't mean three factions wouldn't be easier or easier-to-balance, or that seven factions wouldn't have been harder.
for a color-wheel to work well, you'd want:
[*] An absolute minimum of explicit color-hate cards.
[*] Synergistic strategies for adjacent colors that exploit weaknesses of opposing colors.
which imposes an additional design challenge.
Blackwatch Plaid