Kipnis might have a higher upside (especially with power numbers), but Andrus is a bit safer bet to know what you'll get.
If think you can get 25 x SBs and 10-15 HRs from Kipnis, I'd go with him. As always though, I recommend checking out the probable player pool and seeing who the likely replacements at each position would be.
Depends on the player pool. SS is much more shallow than 2B to me. If there are guys like Aaron Hill, Phillips, Utley,or Rutledge, I'd hold Andrus for sure. I agree that Kipnis has Ian Kinsler-lite type upside, but Kipnis will need to either go into the season with a new approach or get a lot of luck (which isn't out of the realm of possibility, but as it stands, he hits way too many GB). If we are ranking them based on ceiling, Andrus possesses a Jose Reyes-lite type profile with the upside for double-digit HR, and 40+ SB (again, if we are including the luck/growth factor). Remember, Andrus is still just 24 years old. He already has 4 full years of MLB experience under his belt, when many 24 year olds are just entering the Majors. He is primed for a potential big year.
My vote goes to Kipnis. He's going higher than he is worth in most mock drafts I've done, and you could probably get Andrus back for closer to what he is actually worth. Kipnis is probably top 5 or 6 at his position...although Andrus is probably around 8-10 at SS, with Profar lighting a fire under his backside there is a chance he gets traded to a pitchers' park.
I would keep Andrus. You know the floor of what he will provide you, and as stated before, he's only trended upwards each of his 4 years. Kipnis does have more upside than Andrus, but the second half of last year makes me wonder if Kipnis can keep his stats up all year. I owned him in one league last year, and his .230 average in the second half killed me.