When you are selecting a field to be updated or in a criteria and the field is a lookup - you have to "Drill to" the related object.
For example, instead of saying when the "Opportunity.OwnerId" equals... I have to select "Opportunity.OwnerId.UserID" not only does this make for long field names but it can get very confusing.
I also get worried if I'm trying to change the value of the owner or other lookup that I may actually update the value of the related record and not the record reference itself.
It would be nice if we had to options - similar to formula - that let's us either choose the actual record reference field OR drill to the record.