I think it all boils down to personal preference. Personally, I prefer to have some self driving (when possible) & public transport because they all add up to the game & not just mere logistics. In TAR, the winners have a combination of luck, skills & street smarts, & getting about in a different area/country shows all three. Teams have to have good navigational skills and money management so they don't spend all their money on taxis, for example. They also have to think which way is faster to a destination, trust others & take risks because 1 false move can mean the end of them (like when Nate & Jenn from TAR 12 chose to take the subway instead of taxi) but it can also put them ahead of the game (like Charla & Mirna getting all the good flights in TARAS). By providing shuttles & flights, the producers are taking out an element of the race & just bunch people up (almost as bad as last season's HOO although thank heavens this hasn't been as visible this season) IMHO.
As for seeing the race as a competition between teams & not countries, I think if the producers are still positioning the race as a race between teams that represent a country, I'm afraid the majority of viewers will still see it that way. Even the intro mentions the country where the teams come from. It's unavoidable, I guess.