I try to mimic original spoke lengths and nipples to the extent I can do so. On English bikes, I tend to use 12mm nipples because older English spoke nipples on the light roadsters tended to be quite short. On my American-made bikes I tend to use 14mm nipples because that's as close as I can get to the old school long four-side spoke nipples (and the really old ones with only two flats were even longer).

I don't try to compensate for spoke length using the spoke nipple length. If the measurement is that far off, I either buy longer spokes (if they're too short), or snip and thread (if they're too long - I use the Hozan tools).