Just finished my first playthrough of the game... probably shouldn't have started with Flynn's path 0_o
Yeah, aside from TJ's, Flynn's is considered the "worst" route to start with.
If you haven't yet, try and save TJ's for last.
Perhaps a "recommended" order would be: Carl -> Leo -> Flynn -> TJ -> Jenna (by default as it's not finished yet).
EDIT: Just saw further down the devs recommending someone mentioning this play order: The Smoke Room -> Route 65 -> Carl -> Leo -> Jenna -> TJ -> Flynn.
TJ is best played first imo (perhaps even before TSR), especially if you're the kind of player who likes reading in between the lines and tries to predict the twists since it's easy to get tipped off to the twist at the end of TJ's by playing the other routes first. The other reason to play TJ first is because out of all the routes, up until the end it felt like a low budget horror B-movie to me (as someone who played it first), which really plays around with your expectation for the ending. I think if you don't play it first, it looses that B-movie feel and the ending won't really subvert expectations and not be as memorable.
Route 65 I would say is completely optional, and only really matters for Jenna's route. And that's not to mention that a lot of it is repeated in Jenna's route too.
And just to be clear, the devs didn't recommend that order, just that they agree with it.
I started with it. And it was so fucking scary with the monster but I think that It's the perfect route for the beginning. Cuz' you can understand all the Sidneys problems, and the personality of Syd and Flynn, Even you can look at how flynn cares about carl. So when you finish his route you have more questions than Answers and you could know which route would have the answers you want to know (just like me xD that I played Flynn's route and then I played TJ's Route for the answers of what happened)