I do admit, the price penalty isn't the greatest idea and it does punish players that want to build a traditional centre house, but you don't really miss out on new content without pylons.
I do still think that if you where able to craft pylons or use them without any requirements, they would just be pre-hardmode teleporters. Sure, you can use teleporters for fancy things like you use them for, but the ordinary player had a few teleporters to certain places in the world to travel faster. Since teleporters are only accessible much later in the game than pylons, the devs clearly didn't want you to be able to use them however you pleased.
And if someone wanted to build fancy buildings or wooden boxes, it doesn't matter. Pylons only let you fast travel through the world, and as sharkman said he lived without them for 7 years. Both build styles are accepted by Terraria, you can build fancy places in each biome and decorate your world fully, or just make a massive central tower. And you can build simple NPC prisons in spawn or spread them out. Just because a player doesn't want to put in effort into building fancy homes everywhere, it doesn't mean that simple boxes are being rewarded. I build fancy houses for my NPCs and got the benefits of the pylons.
As for the progression, you explore left then right and build a central tower and leave the world as it is. You dont need to explore the surface to unlock NPCs except for the angler and clothier and mechanic. Every other NPC comes after you overcome certain obstacle like killing a boss or getting some life crystal or killing the queen bee. The player isn't "involved in the world" by stripping it off of its materials and building in one place. On my world before 1.4, the corruption has taken 40% of the world and, because I just wasn't bothered to stop it, it spread that much. Pylons encourage players to protect world, aka. what the game is about. The hero protects the world from the evil bosses and corruption. The devs just wanted to add some narrative to the game.