The best legion war suggestion I've yet to see was from a long long while back. Essentially, after the declaration of war by a legion, the opposing legion had the choice of accepting or declining (to avoid strong legions battering on weak legions). Each disable, raid, or hack performed on a member of the opposing legion would be worth a set amount of points (such as disable=5 pts, raid=1 pt, hack=3 pt). Also, planets would be given a score based on the size, rarity and resources that would add to a conquering legions score and be subtracted from the conquered's score.
Go here for a formula that I came up with to rate planets. After a set period of time, the war would end and an official winner would be declared based on total points earned. Most people suggested one week or so, but I like 5 days. Long enough for everyone to get involved, but short enough that it doesn't get boring like most wars inevitably do. A period of less than one week would also eliminate the possibility of bringing in a trader with an uber planet to share at the last second. I would also suggest that only LOYAL players would qualify for points so you couldn't bring in "ringers" after the start of the war. Heck, even base disables could be included with an extremely high point value (because of the red cost in finding a particular legion's base).