I have to agree with those who have already pointed out several important factors:
1.) The VF-0 is much less streamlined compared to the VF-1. Sure, it's nopsecone, pointy feet, and sleek wings look more streamlined, but the body is bulky, with gas canisters blistering the fuselage in several places. Overall, the much cleaner looking VF-1 is the sleeker fighter.
2.) The one and only technology that the VF-0 has that the VF-1 doesn't is some form of active stealth (which is not neccesarily the same kind of active stealth found on the much later YF-19 and 21). When the VF-0 description says 'testbed for future variable fighters' you must remember that at that time the VF-1 counts as a future variable fighter. When the final VF-1 was delayed due to mass production issues with the nuclear engines, they took the jet engine based testbed and put it into combat. That's the way I read it, anyhow.
3.) The official stats, which you can find at the Macross compendium, clearly show that the VF-1 is superior in performance to the VF-0.
4.) The VF-0 looks better in the animation compared to 20 year old SDF Macross animation, this is to be expected. Making it look better with better animation techniques is not a retcon, it's simply better animation. I'd argue that the VF-1 in 'DYRL?' looks just as good, if not better. I also imagine that if the VF-1 shows up in M0, it will look every bit as sleek and nifty as the VF-0.
And to address another poiunt brought up, yes Macross Zero does have incredibly pretty animation, but it does not sacrifice the story for eye candy. I don't even know how that was brought up.