In order to vastly improve dungeons, one complicated solution would be to eliminate instances altogether and have dynamically respawning trash and many more bosses.

This way, if your party wants to go into Toto Rak, for example, you form your party and actually travel to the entrance in South Shroud and step inside. No loading screen. This is the easiest game ever when it comes to getting around the world, so I wouldn't think this is asking much.

Of course this means that other parties might be inside as well. But this is more of a solution than a problem. In order to accommodate such a thing, the dungeons would be forced to be much much larger and more labyrinthine than they currently are.

Finally, for the purposes of how FFXIV uses tokens to buy items, we would simply replace the daily roulette with a quest to go into one of the applicable dungeons and kill 3 bosses. Then, upon turn-in, you get your daily tokens.