So I've started thinking, one of the most popular characteristics of the Persona Games (and by this I mean Persona 3 and 4) is the fact that you can enter in a relationship with any of the other characters. Now, I'm asking because while it's common in the games to romance one of the various gals it isn't in the anime. Also, If I take control of this I might get more flak than an british Spitfire in Nazi airspace. Why? TwilightXFlash:

Now I want to know, considering that you're the guys that are to keep me in check, what you'd think. Are you going to wait till I've written the chapter or do you have any concrete opinions right now?

I'm not shipping them to infuriate readers or to follow some canon. I actually think I can do it, and I want to see if I can succeed where the movie failed.

2399278 Shipping happens, and we're not here to tell you it shouldn't. If you want to do it, do it.

Just uh...don't be surprised if there's a shitstorm in the aftermath. But don't let that deter you!

Just let the characters be themselves, even within the context of the story. If it happens, it should happen organically; if it doesn't, don't try to force the narrative. Given that Flash already has very little character to begin with, which will be overridden anyway when he becomes a Persona protag, it's easier to mold him into a personality that Twilight would be naturally drawn to --so most of your job will be to keep her IC while you build him.
"Shipping" is one thing, but the more and more naturally that you build the relationship, the stronger the impression it will leave on readers. I've read dozens upon dozens of fics that just try to pair up characters, and they're cute, but even if I like the pairing, that's all they are. But when I read a fic that makes an effort into keeping everyone IC, with whatever heartbreak and reconciliation occurs, by the end I'm fully convinced that they're not just a "ship," but an actual couple.

Of course, the above is just a personal preference, and mostly it applies to fics where the relationship IS either a major, or even a central aspect of the plot. One of the reasons the Persona 4 anime didn't "go for" a particular pairing is that it wanted to give equal screentime to everyone, and make every character equally important to the MC, even if they were just friends. So once you start developing the relationship, you should consider how important it will be for the story in general.