Team Rocket is inept, and so is Giovanni. There are unlimited pokemon is wild grass and caves, yet the organisation invests time and resources on stealing pokemon from people. You don't need Red or the Elite Four to go up against Team Rocket. Any trainer at Victory Road can take down the organization just the same. Given that the pokemon centres are free for all to heal up endlessly, even any low level NPC character can eventually take down Team Rocket by making several back and forth trips to the pokemon centres. Not to mention having the ability to create save points and restart until successful, even Thanos will be destined to fail. If without polt holes and plot armours, the rocket grunts should all have pokemon at level 80+ while Giovanni has a full team of pokemon each at level 250. That is what it takes to hold a city hostage. Giovanni will then monetize all the pokemon centres in every city and town. With his empire, only those who pay good money can heal their pokemon and properly train their pokemon to become stronger, while those who are poor remain weak. Red would have been eternally stuck by both Snorlaxes blocking his road towards progression, if not already hindered by his poverty to even afford potions for his pokemon. The entire Kanto will be helplessly praying to celebi to reverse Giovanni's birth from the past, but not have their prayers answered because Professor Oak has not delivered the GS ball to Kurt.
I think you fail to realize one important aspect about Red: his ambition, the be the Best, like no one ever was. Kid at age 12 went to Mt. Silver to train his power further beyond simply being the Champion of Kanto. By the time Giovanni would consider going back in time to uplift his younger self, Red would've wanted his position as boss of Team Rocket....
This would lead to an all time war with Hoenne and I honestly believe Hoenne would win with Rayquza, Kyogre, Groudon, Jirachi, and the Regis. If I remember correct the events in Kanto takes place at the same time as Hoenne. I forget Hoenne has like 2 champion level trainers as well.
