You're never going to like Phoebe for the remainder of the series. Mainly because you will only ever see her through your Cole-tinted glasses. Her weirdness towards her nephew this episode was a bit much but that was resolved at the end of the episode when she became self aware of this. You were supposed to catch the symbolism of that in the scene where Phoebe acknowledges she's doing too much when she hands Wyatt to Piper and says that's her job. And if you missed that symbolism, Phoebe also literally said as much in the later scene between her and Jason Dean. Your deep and profound love for Cole will never allow you to like the Phoebe character ever again. I'm calling it now.
As far as being mad about them not naming Wyatt after Prue...the behind-the-scenes drama between the showrunners and Shannen Doherty was still fresh at this point during the show's original airing. So it's easy to understand why you just don't get it 20 some odd years later. But back then? Prue wasn't mentioned unless she HAD to be.