If you are staying onsite at Universal, you should end your stay there, as it is so wonderful and relaxing (we did this with a Swan/Hard Rock trip in 2004).
If you are offsite the whole time, it doesn't matter, IMHO.
We just returned from a week offsite in a pool home followed by three nights at Wilderness Lodge. Since we were staying onsite at WDW at the end, we did our Universal days (4 of them!) while at the pool home, interspersed with two MK days, then ended with WDW days.