I can't debate the aesthetics. I got my machine late enough that it came with the v3 scoop bumpers and to me it just looks "normal", but I can certainly see the appeal in the cleaner look of using a low-profile scoop protector. And if one type of protection looks better than the other, I have to agree that it's obviously the low-profile ones.
The low-profile ones, if you get them from NinjaCamp anyway, also have the advantage of coming in a variety of colors, so you can add a bit of flair to the machine that way. They do seem to be visually sharp.
That said, and for what it's worth, while the v3 bumpers probably do decrease the number of balls that go into the lower scoop, I have found that for me they increase the number of balls that go into the upper scoop, as well as the number of balls that hit the RUSH standup targets. I've even had some stray balls get deflected into the spinner (which now that my inner loop is working perfectly, is a much more important/useful shot for me ). The v3 bumpers create a deflection/reflection point that, while preventing balls that might have dropped into the lower scoop from doing so, send the ball in other useful directions.
At the same time, I have not found the shot into the lower scoop from either flipper to be all that hard. And I'm not really even that good a player. It's a reliable enough shot for me that it's become part of my multiball strategy, giving me a quick add-a-ball when one of the balls in play drains. So the gameplay downside of Stern's protector doesn't seem that big to me.
Granted, it'd be better if I could just make the shots I want when I want, but I'd have to say that on the whole, having the "fugly" v3 bumpers installed probably nets me more made shots than it makes me miss lower-scoop shots.
Who knows? Maybe one day I'll install a NinjaCamp style protector (though I'll probably print it myself), but for now I find that the Stern-provided solution is pretty much a wash for me in terms of which I'd prefer, since it's already installed (I'd probably feel different though if I were in a position where I had to modify the scoop one way or the other anyway).