I have a few schools of thought; the new way, although ideal for strategic reasons, is not necessarily better than the old No-Choice 1-after-the-other type situation. The Elites are NOT going to hand over an easy match, and will have at least 3 pokemon w/ deadly skills. (Dragonite has Hyper Beam, prove me wrong :P)
I'm sayin, having first choice is seemingly better, the 4 Elites programmed into each game will ALWAYS have their staple element. (Lorelei-Ice, Will-Psychic, etc) If you lose, adventure some more in the given region and rebuild a strong team, but be aware of the elements of the Elites and refix your party accordingly. Say, if Bruno's Machamp is giving you too much trouble, raise a Psychic or Flying type or two to help out.
It only matters only in each given situation. You can only speak for yourself and decide your grand team. P.S. Miltank at level 55+ is a godsend.