Reading TV Tropes... I never realized that Phineas and Ferb had many wasted characters, that could had appeared more, like: Django, Jenny, the Fireside Girls, Mindy (Do you even remember her?), Derek (that sweeden guy), Wendy (Brenda Song), Thaddeus, Thor, Mandy, Coltrane or scenarios that could had been exanded, like Stacy knowing about Perry being an agent or Vanessa and Monty's relationship. What do you think? By the way, I don't see Coltrane as a scrappy, he needed to appear more.
Personally I think the main cast of PnF is already pretty unique and interesting, and that’s where the focus should lie. Some of the characters you mentioned above are simply meant to be characters-of-the-day.
Coltrane is just meant to function as Jeremy’s friend and bandmate, in addition to bringing a High School Musical actor onto the show, since The Baljeatles first aired around Disney Channel’s big HSM phase.
Given how late Stacy found out Perry’s identity, I don’t think there’s much they could’ve done with it. Now, if you revised ATSD to where Stacy is the only one who somehow remembers Perry’s identity, then I think they could’ve done a follow up ep to where she helps him on a case.