To start with, the Stats are: Intelligence, Fitness, Charm, Guts and Bimbo. Guts being what Courage is in Persona.
So is the idea that you go through 5 skits before you get the choice to start bimbofying in earnest? That is, you can start the process physically and make some relatively minor changes, but it caps off until you reach a decision point in skit 6, at which point the physical changes kick off and the mental ones start, too?
If so, that's a good idea. It allows even the players who decide to do a non-bimbo run to still have some sexy optional TF to spice it up a little. I guess 5 Bimbo Points would be the cutoff, with the cap rising to match your level with them from then on?
I think there should be at least 2 stats you could use to solve major problems, to sort of give the player two chances to have a high enough one to succeed. For example, if you go the "pure" route and refuse to use bimbo magic to make Twilight calm down, you can instead use Intelligence, to either reason with Twilight/help her study and make her feel like she's progressing enough that she de-stresses a little bit, or you can try to make a (perhaps slightly more difficult) Charm check to convince her that she's hurting her friends by ignoring her so that she spends some time with them and de-stresses that way (and you could have an option to flirt to trigger the "pure" romance route at this point, much like in a Persona game).
Maybe structure it so that each Social Link has one "favored stat," one that you can use to pass most (if not all) of the major decision points successfully, with the alternative being to pass slightly higher checks for 2/3 different stats throughout the Social Link. So it'll be possible to pass Twilight's SL without high Int, but only if you have at least two other high stats. That way players feel like they aren't being railroaded into grinding a particular stat to get a girl (even though they're being strongly encouraged to).
Though, to make the Good End/Bad End structure work, we might need to add a new mechanic: a unique stat for each girl that represents their progress in their personal mission, with the name changing depending on the character and their route. For Twilight on the pure route, it would be "Stress," and would measure how close Twilight is to a meltdown, and thus the goal would be to make it lower than a certain threshold by passing checks during skits (and maybe stuff like talking on the phone could do it, but by a lesser amount?). If it's too high when you reach the end of her route, Twilight collapses of exhaustion/has a breakdown and needs to be hospitalized, missing the deadline for her program and thus securing the Bad End.
Though it doesn't have to be really bad, it can be you visiting Twilight in the hospital, where she's happy to see you (especially if you romance her) but quickly gets depressed, confiding in you that it's both because of her failure with the program and because she's afraid she's pushed away all her friends, only to have them show up behind you (maybe at your signal?) to throw her a (small and quiet, this is a hospital!) party to cheer her up and show her that they still love and support her. Maybe end with Twilight happier (though still regretful about missing her opportunity with the program), getting ready to write a letter to Celestia and/or Cadance about what she's learned about friendship from all of this...
Whereas if you get her Stress low enough, the help and support of you and her friends keeps Twilight from blowing a gasket and she gets in with flying colors. Her friends throw a big party to congratulate her, and the two of you share a dance (as friends or as more, with "more" being a slow dance. Either way, make sure to mention that she dances like a total dork) where she tells you that she's lucky to have you as her friend. And if you romance her, add to the end a little bit by having her blush and whisper in your ear that she'd like to continue the party later, just the two of you...
As for the Violet Room, I kind of gave some thoughts on that (and other stuff) in the General Writing thread.
EDIT: Then again, implementing this might add too much to everyone's workload. I'd be willing to write some small stuff if anyone wants me to, but I can't code or draw for sh*t.