Much of the actual aviation is deeply flawed. The trench run is just one aspect.

Maverick pulls up to avoid a missile in the dogfight. Airspeed and energy is king in a dogfight, so why give it all up going vertical? He fires flares (good) then splits the throttles to turn around. Possible in an F-14, but also prone to putting it into a flatspin, which is what killed Goose in the first movie.

He gets behind the Su-57, but how? Why the actual fuck did the Su57 not follow Maverick, and instead flew in a straight line so that Maverick could get behind him? Not even a rookie mistake, that's grossly negligent. Maverick fires a missile, Su57 cartwheels out of the way. The plane can actually pull that maneuver, but again, energy is king in a dogfight, and he just threw it all away. It also doesn't do anything to confuse a missile, as it will still track the heat source (the plane's surfaces are still much hotter than the air, so it still has a clear signature). And Maverick makes the not-even-a-rookie mistake, flying directly straight as the Su-57 tucks in behind him. Even if Maverick was surprised - and he shouldn't have been... Russian planes have been able to pull these moves for some time now - he should at least instinctively know to change direction just to avoid the enemy getting right behind him. In fact, if there was ever a good time to fly straight up, that would have been it... The Su-57 would have been so slow, it would have struggled to gain altitude to pursue, and so Mav has time to reposition and re-engage.

Su-57 can't get a lock on the F-14 in the canyon because of the terrain, but Maverick can immediately lock on the Su-57, which has some stealth capability? Okey dokey. And so on, and so on...

There is SO much to pick apart in the movie about the way flying and combat are depicted. Throughout the training, all the way to the final dogfight.

But despite all that, it's still a kick ass, adrenaline-fueled ride. And that's all the filmmakers are asking you to accept.