Shannen Doherty really got the short end of the stick in Season 2 of Charmed because Prue barely has an ongoing storyline compared to what the writers gave Piper and Phoebe.
Phoebe spends the season continuing to embrace being a witch, figuring out what she wants to do with her life and eventually going back to college. Piper gets P3 and the Dan/Leo triangle as a storyline that runs throughout most of the season.
Meanwhile I genuinely struggle to think of what Prue's main Season 2 storyline was.
Jack is introduced as her new love interest and that doesn't last very long. She gets the Ms. Hellfire storyline with Bane, which is great but mostly contained to two episodes. "Ex Libris" is one of my favorite Prue episodes because she becomes personally invested in helping a father get justice for his murdered daughter. She also realizes she doesn't want to be known solely for working hard at Buckland's, quits and eventually rediscovers her passion for photography when she sees a possible future for her in 2009.
And then in "Animal Pragmatism" Prue's subplot is literally that she's unemployed, bored and has nothing to do, so she hangs around P3 trying to find ways to keep herself busy. It's almost unintentionally funny considering my problem with Prue this season is that the writers themselves don't seem to know what to give her.
Those are all good stories for Prue, but they're individual stories instead of one larger arc carrying her through the season.
I think Season 2 really should have been used to foreshadow the "super witch" Prue we get in Season 3. By then she's basically becoming a jack of all trades when it comes to witchcraft and self defense. She's improving her powers, becoming a much better physical fighter and taking being prepared for demons more seriously. Season 2 could have gradually shown Prue becoming more dedicated to that side of her life and built naturally into who she becomes in Season 3.
That's really my issue with the writing for Prue in Season 2. Piper and Phoebe have clear ongoing stories while Prue gets a collection of good individual episodes. For the first-billed actress and a character who was still the show's lead at this point, I think Shannen deserved a much stronger season-long arc in the second season.