Endgame is the bane of LitRPG
In too many LitRPG works, the game-like mechanics are butchered and forgotten as the story progresses, until you no longer have a LitRPG work, just some fantasy novel with few game-like elements.
The story begins with lots of message boxes, and status, and skills learned and character sheet updates. As it goes on and the complexity increases, or the mechanics start to get in the way, or even the character growth gets out of hand, the author begins to neglect this aspect of the work and near the end it is completely ignored by many.
This is a flaw on the design of the game-like system used in the literary work and an oversight by the authors. As the character grows in power, the management of all the status and skills become a big bother (disclosure: I have published one such novel online – not linking it – and felt this nightmare in the flesh), the sense of danger and challenge is removed (e.g. heck, the MC has 30,000 HP and we know a good sword blow deals only 200 damage, no way the villain will threaten him in one blow) and it is this problem that makes authors give up on their game-like systems and just ignore the stats.
There are some examples I can point at of published works that do exactly that, I can post if it is not against the rules.
There's also always looking at the skill tree as something to consider. Rather than making an OP MC that has all of the skills in the game, make it so there's a cap on how many you can have and then encounter someone that took the other tree. The MC has 30,000 hp? Well, this guy took all of the weapon damage bonuses, so now his weapon deals multiple times the damage than anyone else's does. maybe he's a glass cannon with less HP and significantly higher DPS. It's all about balance, which again goes back to "writers aren't thinking like game developers, so of course their MC seems out of whack by the end of the game." Heck, it might even be funny if the MC reaches the end game and, in a situation where it's an actual video game, patch 1.1 comes out and WHOOPS! Your skills got big nerfs, now you have to figure out how to run your build, again, just like everyone in WoW did after every major update. So it's more a flaw with people who write them.
I'm writing this coming off of 4 days straight working on finals with only 6 hours sleep so I hope its legible and I added something to this discussion.
TLDR; The problem isn't LitRPG's but the subgenre of OP MC's within them.