For my upcoming fic, I try to give a realistic timeline of the events as I don't it to conflict with what happened in Sun/Moon and also give a more realistic approach how big/long it is to travel some of the islands. Also I plan to have one or two chapters that will take place some time before the main story's events, similar to how icomeanon6 did with his latest chaptered fic.
Realistic travel time is the most nebulous, frustrating thing about trying to write Pokemon fanfiction. xD I seriously have no idea how big any of these places are "supposed" to be, so that kind of thing I usually decide on a fic-by-fic basis.
As for time-lining, I've found that keeping a spreadsheet has helped in planning what I'm writing right now. For me it's less about travel time though than it is about keeping the characters' ages straight, down to the birthdays. Ages are probably the one aspect of time in my own fiction that I pay the most attention to lately, perhaps to excess. There might be a scene for example where I decide the characters
have to be 13, just-turned-15, and 19 or the dynamic won't fit. And if there's another scene with the same characters that takes place years later, those ages have to be consistent then, too. I want age differences to partially inform the way characters interact (think about how huge the difference between 9 and 10 and 10 and 11 must seem to a new Pokemon trainer), and it was actually a juggling act to get those differences to line up across the entire timeline.
As for the flow of time within a story, for me it really depends on what the story demands. The first thing I (try to) picture when I'm laying out a story is the series of scenes and the logic that connects them, whether that's plot beats, character beats, or the ramp of excitement. If the plot moves smoother or the revelation of character is more impactful when some scenes take place earlier in time than the preceding scene, that's what I go with. I don't think readers in general mind large jumps forward or backward in time as long as those jumps are purposeful. Just as it's important not to jump ahead over important events, it's also important not to feel obliged to dwell on stretches of time that you have nothing to say about. If you have two scenes that ought to be back-to-back for story reasons and they take place a month apart, skip that month because the readers won't miss it unless you give them a reason to miss it.
Mostly-related-rant: It makes no sense to read
The Chronicles of Narnia starting with
The Magician's Nephew. It absolutely guts the effect of
The Lion, the Witch and the Wardrobe for no reason other than preserving chronological order, and
The Magician's Nephew itself works far better when it is answering previously established questions than it is starting off on its own.