so i have some reasons for why i think weird route is "Puppet route"... yeah... i have a LOT OF reasons for this... like characters, story, battles, etc...
lets start from a simple part... characters.

1. some of characters are related to a Puppet! like:
Kris : they are a puppet in mind and you control them with a soul.
Noelle : in weird routh, she just listen to Kris(infact she listen to you) and do some murder and stuff... but she is a Puppet too... because she just listen to Kris... like when she freeze enemies or freeze the puzzles... she just listen to Kris(You).exactly... like a Puppet.
Spamton G.Spamton : Spamton is an actual Puppet... yeah, in neo fight his appearance and everything looks like a Puppet... strings, his mouth, Etc... and Spamton is VERY related to this route... he sell you thorn ring and he is the actual boss of CH2!

so most of important characters are some kind of Puppet. so lets go to another part of the theory... story.

2. story is very simple, YOU JUST FORCING A LOVELY GAY DEER TEENAGER AND EVEN MAKE HER KILL HER GROUP PARTNER-- *heavy breath* yeah... you actually make Noelle to be a puppet. exactly... near the end of cyber city section... Noelle just listen to Kris, she really believe Kris(You) for just killing some enemies... not her friend... even you buy the thorn ring from a actual Puppet(Spamton).

so the story is related to the Puppet too... what about the actual battles?

3. when you get the freeze ring, enemies run away... it means all of the battles arent for killing Fun gang(Kris, Susie, Noelle and Ralsei) ... they are for killing the enemies... yes... and even in battle Kris just defend... and Noelle just doing what you Kris(You) say to her... even in the battle system she ACTUALLY act like a puppet... but other party members do this, right? WRONG!
in CH1 Susie dont listen to you at all, until she finally trust kris and stop fighting for letting kris command her. but Noelle do nothing, AND SHE GO EXACTLLY 180 DEGREE AND DO KRIS'S(YOUR) HORRIBLE ACTIONS, WHY SHE DID THIS? IS SHE STU-- *heavy breath* in fact in CH1 all the kills(using fighting on a enemy and they ran way) dont make you stronger... but in CH2... it makes you stronger, and its 2X for Noelle. yeah...
another thing is that final boss of weird route at CH2 is a Puppet(Spamton).

but there is one other fact too...

4. Kris's power's menu title(in weird route) is "Leader. Commands." yeah... in anyway, someone is controlling a Puppet. like how Kris(You) control Noelle in this route. YOU control her like a puppet in Kris's body.

okay, thats all i had for my first theory. see ya.