Make the ships loud and proud if you want.

Don't make ships at all if you choose.

However, if you make the ships toxic I will come for you. That's not a healthy situation for anyone, so please avoid putting characters in those situations.

A toxic relationship is not something that others will root for. Instead they'll pray that the relationship ends.

I have a character duo that fits this type of relationship:

Andromeda and Perseus. Andromeda, a power hungry young women determined to be more than an alliance, tricked Perseus, her fiancée and husband, into killing her father, and thus she ascended the throne. She accused him of being the mastermind and was one of the first to vote for his death.
Perseus, unfortunately, was an extremely unlucky king.

On the contrast, relationships with ship material are wholesome, enjoyable, and not toxic. They fit together.

Now I'm going to talk about my number one character ship:

Yuri and Jeremiah. She's a reporter, he's a rebel leader. It was the first ship I had ever made in my first fangame and it makes so much sense. Yuri and Jeremiah have similar values and beliefs, though they manifest it in different ways. While they do have a huge height difference-Yuri is 4'11 and Jeremiah is 6'3-they find ways to work around it. They have their squabbles, but in the end they've got each other's backs. I'm rooting for this ship from the moment the characters are introduced.

So, what makes a good pair?

How or why they get along is up to you.

Keep these questions in mind as you make ships:

1. Are they willing to rewrite the stars if it means they can stay together?

2. Will they catch a grenade for the other if needed?

3. Would just being together be enough for them?

Look at different love songs and make more questions from them. If the answer is yes, I'm in full support mode. If it is no, it'll be a while before I'll be on board.

Here's another tip:

Look at any thriving relationship in your life. Maybe it's your parents, grandparents, aunts and uncles, cousins, or your friends. If you want, ask them how they made it work. Use their answers to help create effective ships.

The key thing here is that you want people to root for your ships. They won't do that if your ships are toxic or anything like the stereotypical gay gacha ships.

(It's fine if a male is a cross dresser just don't use that stereotype for them. Chihiro Fujisaki is a great example of a cross dressing character that adds to the story.)

Alright, that's all I have to say here. Again, if you need help with characters please comment below, and now I will also lend my assistance to you for any ship related questions.

Side Note:
Yes, some people do ship some toxic ships, such as Mikan x Junko, or Toko x Byakuya. When I said avoid toxic ships, I said that because toxic ships have fear, hate, maybe even abuse in them, while a non-toxic ship has love, acceptance, and faith in it. Would you really want a toxic relationship in your life? Don't put your characters through that, unless there's a good reason for it in their backstories.
For example, Connor Davis, the ultimate stalker is obsessed with Raquel Morales, the ultimate sweetheart. It is not canon, but it helps build up the tension of the game. People can (I don't know, I haven't written this story out yet-) relate to her emotions towards him.

Think about canon ships from different forms of media:

Percy Jackson and Annabeth Chase

Harry Potter and Ginny Weasley

etc.

At the end of the day, your ships are your ships. Make them however you'd like. I just prefer non-toxic ships.