Is there a way to change the preferences of the "upgrade arrow" in the inventory screen in Skyrim?
Solution 1:
There is no way to change this in the game, unfortunately. The comparison only looks at base values to see which number is bigger. Personally, I ignore it. It was better at lower levels, but now you should use your own judgment.
Solution 2:
Sell off (or store) all of the equipment that is not specific to your build and then the suggestions will be more relevant. But no there is no way to make the game take your armor preference into account.