These suggestions are mainly survival-oriented as I enjoy a nice, balanced survival experience.

Gallifreyan Desert- A simple, new biome (seen in Day of the Doctor and Hell Bent) where an abundance of Gallifreyan sand can be found (texture may have to be orange to match the show's desert or a new block can be added). Perhaps this could be the only place to find Gallifreyan sand to incentivize the player to explore Gallifrey.  Or maybe, Gallifreyan stone is used as the biome's ground block choice and Gallifreyan sand generates the same as it does now.

Barns (and other small wooden shacks)- Structures that can spawn in the Gallifreyan desert. Obviously, inspired by the barn in DOTD, these buildings would be simple uncommon structures containing loot chests. Perhaps the Doctor's spoon and some soup could be found in these chests as a little bit of a gag reward. Other ideas could be farming equipment and simple tools since the Gallifreyans living in the desert seem to be farmers and workers.

Timelords- Perhaps Timelords could only spawn in Citadels since a plethora of Timelords just wondering around the planet is a bit out of place. Since they would be rarer, maybe Timelords could have a functional use. Timelords could unlock the secret of regeneration, so you would have to find a Timelord to learn the recipe for the Elixir of Life. A few ideas for how this could be done: a trading system, a leveling system where you have to "talk" to several Timelords until you finally unlock the recipe, or maybe they simply provide an alternative way of obtaining the Elixir (which means the current recipe is still in place and obtainable exactly like it is now). 

Small idea: A destroyed variant of the citadel can generate rarely. As in reference to Series 12, the Time War, or both.