Laurent, I'm not saying that your ideas and suggestions are stupid, just that they'd seem out of place. Nor am I opposed to other forms of transport so long as they're tastefully done or for progression of plot. Example of progression of plot: character must infiltrate a base that is surrounded by a mountain range, making it impossible to get in by foot. A third party may want to gain the valuable information inside so they decide to ferry you in by a captured Vertibird or something along those lines which is destroyed upon landing or is only usable for one time. The point is that the use of the Vertibird would be isolated to only this particular point to allow the plot to progress.
And, outside of setting misplacement, certain forms of transportation wouldn't be practical for gameplay balance reasons. Like I said, I was always leery about the car from FO2 but, in part, it was kinda useful (not essential, however) in the whole Karl/Modoc/Ghost Farm resolution. But after that point, the car only became a convenience while traveling abroad. And the timing in which the car was introduced was a well-planned thing. In the beginning, when you need the EXP, traveling on foot is a slow process, rife with the possibilities of random encounters. Later on, when you've been beefed up a bit to the point where the majority of EXP earnings are through quests, the car can let you get by some of these random encounters, which just become nuisances.
If there were a time limit which you must meet (and I really, truly hope there isn't) and you're in dire need of getting somewhere fast, then sure, you'd want a speedy transport.
These are the things (setting/plot/gameplay balance/timing) that have to be taken in account when introducing something that can affect the gameplay.