It's pretty complicated. Long write up incoming.
Planning
Ultimately, the planning/scenes/story beats are kinda normal. You have set pieces, and you work your way through there. But I think the cool thing about LitRPG is that you have a bigger set options, it's just that authors tend to rely on numbers/stats waaaay too heavily for any meaningful growth. Those things should accompany the story, even if it's the focus of the genre.
Planning also ties in with the power progression.
This is just one folder for planning.
Power Progression
MC's obviously going to get stronger, as is everyone else, but you really need to be careful with it. Too strong too soon and the story's a write off unless it works well with the story itself (like Overlord. MCs OP, but the story itself complements it). Bad LitRPGS get stuck on this and there's pretty much no meaningful threat/development at all. For me, there's always the psychological aspect to tap into (it's a major point of the story after all), and other means (i.e, technology, emotions, and a plethora of other... eldritch, existential-threat-kind of methods).
It's reflected in stats, attitude, mentality, resilience, etc - not just numbers. MC used to be a non-violent healer, now they're considered the most violent and has a taste for blood (literally, since eating is their biggest asset). MC needed to break down and come to terms with this, and still laments it but to a much lesser and professional degree (psychological progression) - Also progressing from human to whatever they've become.
Funnily enough, I do not update the stats that often. Just at major points.
Basically: Yes. I plan the power progression step by step.
Skills on the otherhand is a mix.
Skills
Some skills are there to complement the character, others are set pieces waiting for their payoff. Something like 'cooking' wouldn't need one as large as something like 'Appraise Object', which periodically reveals missed information vital to the story as it gets stronger, or Punch which had a payoff of being the MCs laughably pitiful skill to being one of their strongest moves, as well as setting up another major set piece awaiting its payoff.
Every skill gained serves a purpose as well, and ties massively to the characters + their personalities. Skills are actually an indicator to tell what sort of a person is like. For instance there's a violent tomboy character that's completely 'manly', but has skills that suggests they're far more feminine than they are (like berry picking, weaving, etc), which clues us into their real selves and subtly sets up their sub-story.