I always consider whether I think I'm actually going to need the alternate or not. Sometimes you are carrying an alternate because it is a legal requirement but all indications are that you can expect to land at the planned destination, other times you foresee a good chance that you will actually be going to the alternate. So in the first case I'd choose the alternate that meets all the legal criteria and is the most economic for the company, in the second case I'd choose the one I'm most comfortable flying to. Sometimes the decision is not mine and the company will provide their preferred alternate out of those available.