I can't believe I have never noticed this before. The Seer wasn't out to get Phoebe's baby's powers in order to rule the Underworld for herself, her ultimate goal was to turn TCO into the selfish,whiney, unitelligent people they became in later seasons.
You see, the Seer had a vision where she saw TCO doing many great things and saving many innocents and becoming the greatest force of good ever known. Being evil and all she couldn't let that happen so she went after the most vunerable sister first.
She manipulated Phoebe into picking Cole over her sisters when he became the Source thus ensuring that Phoebe would become PhoeME and think about herself before her sister an innocents. She made sure Cole became the Source so Phoebe would not try to find a long term relationship and get with every guy she meets thus ensuring her evolution into Freebie.
Turning Phoebe into Queen of the Underworld was how she got at Piper. She knew after Prue died Piper had to take the burden of being the oldest and Piper felt like everything was agains't her. Making her sister turn evil and made Piper feel even worse about herself, slowly degrading her into the whiney, self-centered person she was in later seasons.
As for Paige, she made sure with Phoebe evil and Piper feeling sorry for herself, Paige had to take the role of innocent saver. She knew if Paige had to stop the demons by herself she would get pulled more into the magical world and eventually that made Paige quit her social worker job. With her taking up magic, her IQ points slowly dropped and got herself and her sisters in trouble a lot.
You see, the Seer was doing more damage than we initially thought. TCO may of vanquished her, but her ultimate goal was completed, to destroy our beloved Charmed Ones, and to destroy our beloved show.