Found this nice little sandbox demonstration video fhe Phoenix upgrade in action vs. Mutas.
Long story short: the difference in unmicroed upgraded phoenixes vs microed upgraded phoenixes is noticable but fairly small. But when you actually attempt to micro them both, the difference is huge--the normal Phoenixes still die quite quickly even with active micro, but the upgraded Phoenixes can kite continuously while taking next to no damage, and since they aren't taking losses they just mow through the muta ball at a really high rate (skip to 2:45 in the video to see what happens with even basic micro when you use upgrades phoenixes vs mutas).
When combined with the ability to magic box vs. fungals, and Zerg actually has reason to be afraid of Phoenixes now.