Mathematically, it is more beneficial to upgrade the lower drill. However, I prefer to upgrade the most expensive option because you can't really enumerate the difficulty of saving up enough elixir for the more expensive drill vs the cheaper one. Here is some math for you:
lvl 1 to lvl 2 drill:
Loss:
...20 DE for 1 days time
Gain:
...Increases 10 per hour
Opportunity Cost:
...20 DE * 24 hours = 480 DE
ROI:
...480 DE / 10 = 48 hours
lvl 3 to lvl 4 drill:
Loss:
...45 DE for 4 days time
Gain:
...Increases 15 per hour
Opportunity Cost:
...45 DE * 24 hours * 4 days = 4320 DE
ROI:
...4320 DE / 15 = 288 hours
lvl 5 to lvl 6 drill:
Loss:
...80 DE for 8 days time
Gain:
...Increases 20 per hour
Opportunity Cost:
...80 DE * 24 hours * 8 days = 15360 DE
ROI:
...15360 DE / 20 = 768 hours
Edit: formatting

