Game mechanics need a more realistic reinterpretation, that is
Gameplay and Story Segregation, understandable reasonable and logical to do so.
But unable to keep consistent with the reinterpreted rules is just purely
Mechanism Inconsistency, that is another complete different issue, because
consistency is the most important key element to suspend audience's disbelief. Without it, doubt is arouse and audience shall waste time on questioning "
What the hell......? How did they do it?" continuously rather than using the time to enjoy the show.
So how do I feel about this issue of anime contradicting game mechanics? If it has a better reinterpretation, I'm fine with it. But if they are unable to keep consistent with it, I then have a problem with it.
BTW, on another contrary, I would had prefer it better if the anime didn't bluntly mention nor show the gameplay mechanics at all during the run. Don't tell me electricity is super-effective against water, no effect against ground. Don't tell me Infernape's ability is Blaze, and it triggers when its HP run low. Don't tell me MegaBlastoise's attack are much more stronger thanks to its Mega Launcher ability. Don't show a poison icon effect on Charizard after it hit by Venoshock, and then with a healing light effect showing its status is healed by consuming a Pecha Berry. Don't show a red/blue glowing effect to signify a change in stats modifiers. Etc et cetera.
You can still have the mechanics presented, but just reword it in a better phrase such that it sounds more organic and realistic, rather than being digitally systematic and robotic mechanical. For example:
"What!? Pikachu's electric attack is not working!?" "Fool, Sandshrew's body surface is insulate to electricity, you are not even scratching my Sandshrew with such useless attack."
"Get up, Infernape! This is not the end yet. Show them your underlying power!" The injured Infernape stand up and roar loudly to the sky, unleashing a powerful fire attack much more stronger than expected despite its damage it had already received.
MegaBlastoise launch a super powerful Dragon Pulse attack. "It is surely very strong as expected. No... may be stronger than just the pure effort of Mega Evolution. Probably the cannon on its back helped in strengthen the attack as well."
Charizard hit by Venoshock, and its body is wobbling upon standing. "Charizard, are you OK?" Charizard nod, but its sickly expression couldn't hide the fact that it is poisoned. "No, you are not OK at all. Eat this, it shall relieve the poison you just received from previous attack."
Stats change? There isn't even things like parameter statistic, how to quantify stats change? No need of any glowing effects.
Please, anime world on TV-screen is not game world on game-console-screen. Take away all the systematical mechanics and inorganic portrayals.