Well, I think many seniors here have given proper and good advices, so I just want to share my recent experience.
Recently, I made a story with an unusual concept (at least I think so). I've prepared the plot and the twist, also planned where I wanted to place the hints, but I couldn't do the scenario properly due to the time limit and my condition. In the end, I had to cut most of them and it's just like it ended where it's just about to start. In short, it's an epic fail. My proofreader told me that if I don't have the time to fix it, then just throw the idea away and make it a simple slice of life thing, and focus more into each character. I agreed.
To come up with plot twist and interesting ending concept needs time, to arrange the outline for plot needs more time, to execute it once until the end needs more more time, and to be reviewed and to fix them need extra more time. Before you decide how the story would end, I suggest you to ask yourself, how much time and effort do you want to use for this project. If you have no problem with this, then I can suggest you some things :
1. Read as many stories, or watch as many movies as you can.
2. Try to be the characters as you create them. If you want to build a mystery like murder case, arrange the real chronology from the murderer first, then set the clues.
3. Don't forget the characters' identity and development, just for the sake of plot twist. Uninteresting characters can lead people to leave your story before they can get to the first clue.
4. Write the setting of all important characters or you will forget their role in the writing process. You don't want that to happen. You have to decide the ending for each character before you write the whole scenario.
I like plot twist and unpredictable ending more than cliche stories, but it doesn't mean I don't like cliche stories.
Some film I watch and I like are cliche but have a good characters, character development, deep story, etc. While perhaps I can predict how it will end, but the journey for that to happen is so entertaining that I don't really mind for it.
About the cliche story you told us, I don't really think it's so bad since it's still general.
So, you have a princess sneaked out of the castle, joined a pirate crew, went on adventure, and saved the world.
This princess is actually the strongest of all people in that era, no one can defeat her in, well, let say in swordsmanship. Bored, she sneaks out of the castle, being told about some legend in the sea and joins a pirate crew, searching for that legendary place. Eventually, she finds out that she isn't from that world and the world she came from is actually destroyed by the kingdom where she has been lived for these past years. Some of her races survived and want revenge, while she's confused. So, which world will she save? Well, I don't know. It's just me and my stupid idea.
What I'm trying to tell is, with more detail and more characterization, I think people still can change the cliche concept to be more interesting. A princess joining pirate crew itself is interesting enough, though. I wonder the world setting you've imagined