The characters are the best part of the game! It's awesome that there's character development, especially for most of the main team. I think I'm way too enthusiastic about them. Sooo, I apologize in advance for the tl;dr. :P
As for my favorite, it's gotta be Emolga! He brings a lot of character to the team and shows that a team may not always get along. You can see that he really cares about Dunsparce through his interactions with him and Virizion. This is exemplified in one of my favorite moments: the expedition to the Great Glacier. Although he's serious when it comes to Dunsparce, I like his joking nature; it helps makes the team really feel like a tight-knit group you care for.
Another one I really like is probably the one that Richard's talking about.
Then there's the partner. In my opinion, the best partner in all PMD games! He's just so dedicated and forms such a bond with you. By the end of the game, you just have to feel for him. During the post-game, I found it especially sad to see him
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For NPCs, I'd have to agree and go with SIR Quagsire, Scraggy, and Victini. I also want to add in Herdier. Scraggy's interactions with Quagsire and Victini are fun. And of course, da dadadahhh V-Wheeeeeeel! Herdier is the sane 'mon of Post Town, and he
Also, his Scottish accent is fun to read (but super hard to say aloud!). :)