There is no reason to fly short distance if you want to go from city center to city center. However, if you're already arriving or leaving on a long distance flight, the whole overhead of getting to/from/through the airport disappears and those 1.5 hours start making a difference. I think forcing companies to advertise more honest flight durations and prices could make a huge difference. If the airline tells you that…
I largely agree. One issue with France is that their train system is very Paris-centric. Want to go from the Rennes northwest to the Toulouse in the southwest? Yeah, you’re going to go through Paris in the centre of the country. Same with Bordeaux to Lyon. Takes about the same time driving as high-speed rail takes a horseshoe route.
(Admittedly, a Bordeaux-Toulouse-Montpelier-Marseille-Nice connection in the south is probably a viable TGV route. But at a quick glance, that's probably the only viable non-via-Paris route I see.)