Looks like an interesting premise. Sounds like an alternate universe where Arceus didn't want humans to rule (hmmm, I wonder why - I hope you'll expand on this). But why Ralts? What makes them fit to be the ruling species? Did it just happen that way, or did Arceus choose them because they're sensitive to others' emotions so they'd be better than humans? Why are they of different elements, and how does its element get chosen? When do they have this ceremony? Why can't males evolve into Gardevoir? These are really interesting questions and are important for world-building, because you want to show that there are reasons behind your choices aside from "but I wanted to," and I'm not sure you've thought about this stuff just yet.
Unfortunately, it's hard to comment much on your plot at this point, so I'll get into specific ntpicks. Try not to be discouraged by them; no writer is perfect when they start out, but the important thing is to learn from your mistakes. Take the advice you get and use it to improve your writing for the future.
1) Use a spellchecker. You have a lot of silly spelling mistakes like "arival" and "strenth," which wouldn't be there if you had proofread your work or used a spellchecker to find them for you. That's also why you should be writing on Microsoft Word or a similar program - it allows you to both save your work so you can edit and proofread it, while also checking for mistakes you may have made. Please start using it.
2) Capitalize the right things. Names of characters, places and Pokemon need to be capitalized always because they are proper nouns, plus the word "I." If it's not a proper noun, it doesn't get capitalized - be careful, since you capitalized random words here and there. So "Arceus," "Alpha," "Omega" should always be capitalized because they are names, and you have to be consistent with whether or not you capitalize the names of Pokemon species, because you weren't consistent with " articuno, zapdos and Moltres." Either capitalize all species or none of them.
3) Be careful with how often you use ellipses. Having "..." once or twice is okay for dramatic effect, but if you use it too often it loses its effect and just looks lazy.
4) Be careful with commas. You actually use them quite well most of the time, but you're in the habit of using them to give the name of something, such as "which they call, Nillia" and "The Ralts Live in a floating city called, Soaria." There should not be a comma or any other kind of punctuation here. Otherwise, you use commas perfectly!
5) Learn how to use colons. You can only use : after a complete sentence, which means that if you replaced the colon with a period, it would make sense as a complete sentence. For instance, take "Soaria, is supported by an ancient Jewel called: the Shard of Alpha." and replace the : with a . and you'll see that it doesn't make sense. Almost every time you used a colon you can literally just take it out because it's unnecessary.
6) Don't use parentheses for important information. If you present (something important) this I just did, you signify that it's not actually all that important. But the name of the world they live in and other such things is very important, s it shouldn't be in brackets this way. In fact, you should rarely use brackets in a story.
7) Write out numbers if they are smaller than ten. So instead of "5" it should be "five."
8) Just keep in mind that you need to hit the enter button twice after each paragraph, and that each chapter of your fic must be at least two pages long on Microsoft Word (another good reason to use the program).
These are all very basic things you need to know when writing, not just for fan fiction but also for school, important e-mails and letters and so on. It's all pretty basic stuff, and it's easy once you get the hang of it.
I hope you'll make the right edits to your story and keep this in mind as you continue. It sounds like you have an interesting concept going, and you'll be taken more seriously and get more readers if they see you putting effort into your writing. Good luck!