He had seen alot of it, if not all of it during his journey.
“Alot” isn’t a word – it’s “a lot” (this mistakes also shows up when you say "It would've saved him alot of trouble") This could be better worded as “He had seen most, if not all
But now that was pretty much over. After three years of almost non-stop traveling, he had begun to feel homesick. A feeling that was new to him.
Like I said, sentence fragments are okay to use every so often for emphasis, but if you use it them a lot then they lose their punch. A fragment is really just any time you have a phrase that doesn’t really make sense on its own. Your first and last sentences in this quote are essentially fragments, but while the first one works well, the second one doesn’t really. All you have to do is join “a felling that we new to him” with the previous sentence with a comma or dash, since it’s a complete, singular through, or you can just tack on “It was” and keep it as a separate sentence. Only use fragments when you want to really emphasize something every so often – overusing it takes away the impact.
he had begun to grow re-accustomed
You can just say “accustomed”
Pikachu, of course had stayed with him.
The phrase “of course” is off-set, so there should be a comma both before and after it, so it’s “Pikachu, of course,
had stayed with him.”
Not the traveling that he had once loved though. Traveling that he had never been used to. But that was all in due time. All in due time.
You need a comma before “though.” Also, I see whta you were trying to do with repeating “All in due time,” but it comes across as a little cheesy.
"I worry too much.
He told himself. After all, he did look like he had changed his way's."
Is mew actually saying
“he told himself”? Always put quotation marks around spoken words so we know where the dialogue begins and where it ends.
Also, whenever something is pluralized (more than one), you just add an s, not ‘s. So one way, two ways
Mew was trusting him. That was his first mistake. And with Mewtwo, you can only make so many mistakes before he snapped you into his trap.
The first two sentences really don’t need to be alone here, so you can change the period after “him” to a semicolon. Semicolons join two complete sentences, so it would look like “Mew was trusting him; t
hat was his first mistake.” Also, you randomly changed verb tense in the last sentence – “make” is present tense, but “snapped” is past tense. You can change it to “snaps.”