Here's an unpopular opinion: Unova's circular, railroading region design isn't that bad to me, especially compared to other games. This is going to be a long post, and it will cover all the times you can go off the beaten path in all the main games save for the postgame (in every game save briefly Johto) which in almost all games are pretty plotless save ORAS and USUM, and by definition optional if you just want to beat the games and be done with them.
A very nice, long read, but I feel I should chime in with one aspect you didn't consider: the opening of shortcuts later on, making the region traversable by foot, which again means you won't need Fly if you want to revisit areas quickly. The option to hop on your bike instead of teleporting from place to place makes players experience the region more, revisiting or at least passing by the places the region has to offer. At least for me, it makes me feel more at home in the region, I get to see its various locations instead of the Fly cutscene over and over again.
Kanto is especially notable here, with the map opening up for travel between most cities (save Pallet, Viridian and Cinnabar) within a couple of minutes (although you have to have a Repel and Cut if you want to get to Pewter quickly from the central areas). In Johto, you can also bike pretty quickly between Violet, Goldenrod, Ecruteak, Olivine and to some degree Mahogany (again, Repel is needed for the latter). Hoenn has Rusturf Tunnel, Cycling Road, the surf bits of Route 103, and a convenient boat service between Slateport and Lilycove to make most cities connected pretty quickly.
Sinnoh is where this started to fail. Not only were the areas of postgame interest placed on diametrically opposite sides of the map (Pal Park, the Battle Tower and the Day Care), but there were really few cities you could walk between without traversing lengthy routes (possibly full of unavoidable grass), or caves, or those god-awful HM barriers or Mount Coronet which featured unholy amounts of all three. You needed tons of Repels and HM slaves to go anywhere over land in Sinnoh, which makes this my least favourite region to date.
Skipping Unova for a second, Kalos has very little in the way of quick travel too, but the hub-and-spokes layout of Lumiose City and its surrounding areas puts many cities within a short bike ride, and Connecting Cave lets you go from Camphrier/Battle Chateau to Cyllage pretty quickly. If only the Couriway rail station had been functional, you could have traveled quickly from Lumiose to the three cities clustered in the east pretty fast too. Still, it's not a very pedestrian-friendly region all things considered.
Alola has very few settlements, and the biggest ones can all be reached with a ferry, so it's doing fine in this regard. The first couple of islands are also easy enough to circumnavigate on foot. However, only one shortcut really opens as the game progresses, the one that lets you reach Royal Avenue from Heahea City without passing through Paniola Town.
Unova's big circle is mostly easy to traverse (Twist Mountain and Chargestone Cave form a tedious barrier around Mistralton City, but it's the only really isolated town), but there is nothing to reduce the distances between cities, meaning you'll be biking for a while to get anywhere. The distance between Nimbasa and Opelucid is short as the crow flies, but you'll have to pass through six routes, three towns and two bridges to get from one to the other. True, there is no unavoidable grass between the two cities (as long as you have Cut for Route 13), but it's a very long way to go. To a lesser extent, this is also true for the areas you want to travel between in the late-game, like the Day Care, the PWT, Join Avenue and Battle Subway. Again, no unavoidable grass between them, but it's the same long trek every time.
As each individual route is well suited for overland travel (no unavoidable grass, hooray!), I may still opt for a bike when traversing Unova, but while doing so I keep pining for some shortcuts. If only the Battle Subway had a functional line!