Phyrexian mana gets a lot of grief as a mechanic, and I do think it has a very limited scope as to how much it could really be used and still make for interesting gameplay. There are multiple factors at play here and it might not be possible to disentangle that mess. For one thing, a lot of stuff in that block created the atmosphere of being
just wrong and made people uncomfortable, but that was also explicitly what WotC were going for. Mark Rosewater has said many times that they wanted the Phyrexians to feel creepy, that they wanted players to feel a hint of fear and dread when going up against them. So I guess they succeeded? Looking strictly at the actual cards, most Phyrexian mana isn't a real problem and some of those cards have interesting applications. And others are victims of circumstances. Birthing Pod drew controversy in Modern because it was Birthing Pod, not because of the Phyrexian mana symbol specifically. Gitaxian Probe drew controversy in Legacy because of a confluence of different things. Really, the only Phyrexian mana spell I personally view as a problem is Mental Misstep, and that's because it throws off the balance of countermagic. Normally, there's a hidden deckbuilding cost to focusing on countermagic: you need to hold mana open to use it, so you need your other spells to be instant-speed in order to accomplish that. The only exceptions, historically, were cards that set you back on card advantage (like Force of Will) or ones that set you back on tempo (like Daze). Using life as a cost isn't truly
free. A lot of people underestimate the cost of paying life for something in Magic. But the danger in something like Phyrexian mana is that it's probably bad for gameplay if it can completely circumvent
opportunity cost. Circumventing opportunity cost is extremely powerful, and usually it takes a combo to do it. The now-defunct Vintage "GushBond engine" accomplished it, turning Gush into a spell that one could put no mana into, get mana back out of, and draw cards. But if one card, by itself, dodges opportunity cost, that's when I think we run into trouble. Most of the other "free" Phyrexian mana spells are more conditional. You do gets something from them, but it tends to be pretty minor outside the scope of special combo or engine.
I don't know. I think I see a distinct difference, but maybe it's just my bias. Is it feasible to say that Mental Misstep is a problem because of Phyrexian mana, but Gut Shot isn't a problem on that same basis?