The downside is that War Mode will make you vulnerable to other players, which means you might be killed more often. Whether it’s worthwhile will depend on the zones you’re visiting and how active the other faction is on your server cluster. Heavily populated realms usually mean more players on both sides, and more conflict, but on quieter realms, you may rarely run across an enemy.
Usually it's best to avoid a lot of instance runs. It is too difficult to account for bad groups, and some instances are too far away with too few quests. Since the experience is very good, it's a good idea to clear nearby instances which have a lot of quests once (Gnomeregan, Deadmines for Alliance). Distant instances with few quests should be avoided (Deadmines for Horde). Low level instances can be cleared by paying or befriending a single high level character. However, since patch 3.3 a new Dungeon group finding system has been implemented, as well as a direct port to dungeons (when entering the group you get ported to the dungeon and back to the same location if you leave it) and thus the travel time to dungeons has been greatly reduced. This makes it a good idea to complete quests or grind while you wait for a group to become available.