"That Which Survives". It's a great story where it counts the most, but it is too simplistic with just Losira skulking around. With the dough, they could then add to the plotting as now the computer can generate more than one killer guardian simultaneously, with more than one actor, and get around split screen problems too. It'd be a better cake as a result. Even then, kudos for the production team raising the stage and rocking it - that was really cool and far better than everyone swinging in some choreographed direction. Ditto for Losira's teleportation effect, which scared the Charliedickins out of me at the time, and still holds up - all things considered. Now imagine four or more going after the crew, that'd really ratchet up the tension...
"The Doomsday Machine" is just too easy, though it's definitely a fun one to get that treatment thanks to what TOS-R showed.
"All Our Yesterdays" as well as they could explore time periods more and other than just rummaging through the wardrobe and backlot to find 16th century stuff. Again, great core idea and overall robust execution, but more could have been done and that'd be another neat 2-parter. Think VOY's "The Killing Game" where they finally did more than other than relying on the same-old (though they wallowed with WW2 and didn't they go back to that sweet sweet well o' Wolf-359 as well, for a bit?)