I don't really get the transporters/shuttles argument. One if the things that irritated me in the new films is that they overuse shuttles, for example when the crew flies up to the orbiting Enterprise rather than simply beaming. Sure, the new films have the budget which the original show lacked, so to can afford to have the more visually impressive shuttle take-off and landing scenes, but it doesn't make much sense to spend so much time and energy ferrying people up in the midst of a crisis.
Star Trek has always used transporters as the primary means of travel to and from a Starship. Shuttles are used for short to medium range interstellar trips, not for planetary exploration except for in certain circumstances. Why would you need to do an "aerial survey" when you have powerful computers and sensors (located on the bottom of the ship for just that reason
) that can discern individual blades of grass from planetary orbit? It's a waste of energy, time and resources.
Likewise with the helm console, it's all powered by the supercomputer in the heart of the Enterprise. Chekov just tells the computer where to point them, and Sulu says how fast to go. No wonder by TNG they no longer needed two staff for those largely automated tasks.
Basically all your criticisms seem to reflect your underestimation of the power and capabilities of the ships as depicted in the series and films.