I have thought about this subject several times and even thought about starting a similar thread.
Thus, please allow me to share my ruminations (i hope).
Gamer body.
Generally means a body that shares characteristics with a video game character in their physicality.
HP/Life points pool that depletes without any real consequences, maybe if you want with a cosmetic decal indicating 'damage', or if you want to grant a factor of tension in the system, granting de-buffs when they deplete significantly. Usually with increased healing, sometimes things like complete healing, including regeneration of lost limbs after a period of sleep.
Other times just absurd passive regeneration without any need for sleep or rest at all.
Granting the gamer 'gamer body' must mean they are no longer able to get stronger outside of the system.
I have seen several stories where the gamer has the ability to get stronger both from the system, and they can then do normal stuff, like weight lifting for stats.
Personally those consequences while minor always stand out to me.
Whatever you decide, describe it in detail, the system needs consistency if not transparency.
Stats.
Some stats generally usable in RPG make no sense in a narrative story.
In my opinion mainly Intelligence and Charisma, through Luck can also be iffy.
Using intelligence, from DnD as an example.
10 points being the average (around 100 IQ).
20 points being the absolute maximum for a human, I know there are templates and other modifiers, but just for an example's sake. (let us go into super genius, superhuman territory, and say 200 IQ).
Writing a 200IQ character would be extremely difficult. But what if the system is generous and our character gets points for noticing that Earth is round and calculating change from groceries in his head. How would a character with 45 INT even express themselves? I know this is only fanfiction, but assuming we want some sort of relatability in our stories, how do we write a 450IQ person. How could we even imagine that? That would be existence so different to us, we could as well write them as an alien. Those of us that remember the difference between high and low INT run in fallout/fallout2 will know what I mean. Ok, rant over.
Similar problem with charisma, while it might be a dump stat for some, in a general gamer story, soon conflicts would become unresolvable because all animosity ends with one MC smile. You are effectively turning your character into a mary sue, so likable even their enemies cannot help and be charmed by them.
Luck can be a fun thing to play around with, especially when it's low. However, in a setting overflowing with stats soon you will end with a xianxia protagonist tripping over charms, legendary herbs, and secret scrolls.
Of course, if you use a system that is sparser in stats, like dnd, where even 5 gained stats are not that big of a deal this might not be a problem.
In place of Intelligence, I would propose to use something simpler, like 'ENERGY'. Instead of determining their intellectual capacity it would simply inform of their potential output, be it mana, chi, stamina, or whatever your story needs.
Another good mechanic would be perception or insight. Instead of just being smarter, or spamming observe onto everything, plot-relevant, interesting things either 'get highlighted' which is a very 'gamey' thing to write, albeit transparent in its introduction, or simply are 'pulled into attention' of the mc.
Intelligence, Charisma, and Luck should generally be either excluded, locked as stats, or possibly hidden.
For example, doing something actually mentally taxing grants our MC the ground +1 Int, even though they do not have it on their sheet.
In my belief (even though I abhor the idea of an INT build mc acting with 1000 points the same way they did when they had 50) in the end, everything can be made to work, as long as you plan for the development from the beginning. Do not write yourself into a corner by turning your MC into a god-smacking superbeing in 5 chapters or you will lose all tension. CHR or LCK build mc can be a fun crack story if done properly. In the end, even Kishimoto needed several retcons and somehow ended with Madara getting merc'd by a deus-ex-machina because he wrote himself into a corner.
Now my idea of a sensible system:
- the character needs to eat, sleep, shit etc, albeit as they progress those needs lessen
- since obtaining the system gamer no longer can get stats outside of the system
- damage is regenerating constantly, while resting, getting medical help it can be accelerated
- potions for battle situations exist but are rare
- permanent damage (burns, amputations) also regenerate but slower (25hp of severe burns regenerates as 75hp; amputate hand is worth permanent 50hp, and will regrow, but is worth 500hp)
-no quests, or very rare quests. I believe that the window appearing instead of an everyday chore should be something huge.
Example of stats:
Strength - physical strength, lift, carry capacity
Dexterity - skills in performing tasks, nimbleness
Constitution - overall physical build and durability
Perception - the ability to notice things
Energy - overall energetic output of the character
With possible INT, LCK and CHR or attractiveness as hidden or locked stats.
Here we come to the question of secondary stats.
Speed could he STR + DEX, or (STR+DEX)/2; or if you want to use Chi/Chakra, add Energy to the equation. For example for your Naruto gamer, Speed could be (STR+DEX)/2+ENR/5
The idea is for secondary stats to be the effect of 2 or more main stats. Like coming back to Naruto Chakra should be derived from CON and ENR.
Other possible secondary stats:
hand-eye coordination, durability, throwing, insight, etc just look at a dnd or a fallout character and pick what you need for your story.
Instead of leveling via character levels, everything would be conducted via skills.
Skills have x (depending on what meaning you want to give stats just pick a number between 10 and 100)lvls and come in 5 grades.
☆☆☆☆ - (D) skills - always grant +1 stat and proficiency - common skills,
★☆☆☆ - (C) skills - always grant +2 stats and profficiency - slightly more complicated skills
★★☆☆ - (B) skills - always grant +3 stats and proficiency - generally intermediate things, stuff like punching, playing an instrument come here
★★★☆ - (A) skills - always grant +4 stats and proficiency - advanced stuff comes here, things in this bracket should have prerequisite skills.
★★★★ - (S) skills - always grant +5 stats and proficiency - expert stuff, skills here are either evolved or need several prerequisite skills.
✪✪✪✪ - (EX) skills - you will probably want to go wild, 'named' skills come here. The absolute apex of a skill.
Obviously more advanced skills are harder to level, but also grant more feats, compared to less advanced ones.
Feats should be either activated or narrative things instead of statistics.
Some skills have no advanced levels. Cooking would end at a C grade for example.
Some skills could be self-taught, others would require a teacher.
Punching, kicking, dodging, and blocking would start at D and scale up to B, having all of those mastered D, would allow picking a general martial art that starts at C and scales to S.
Boxing requires a teacher or a manual and punching, dodging, and blocking at minimal C, but it starts at B and has better skill gain than 'self-made' martial art. But Boxing ends at S, and with a great personal cost, you can 'evolve' your personal martial art into EX, either picking something from a game, anime, or designing something completely new.
I know this probably makes little sense, but it's just a general outline of something super flexible that was bouncing in my brain for some time without actually codifying it.