Being an avid player of both War and Rune I suppose I'll weigh in here. I also have played War with 3 and 4 players, while I will say that 2 is deffinately the best and how it is meant to be played I also really do like the 4 player game (3 player not so much). In a 2 player you can really just focus in one area if you want to, while in a 4 player the sides resources are split up a bit more, as such it is more likely for stuff to be happening all over the board and make for a rather interesting games with a decidedly different feel from the 2 player. That being said, War is perhaps my favorite 2 player game of all time.
Now for Rune, I just love everything about this game. It has a quick and dynamic set up. Conflict right off the bat. Heros, and so on. Game play is fast and interesting with very little down time. One of my games described it as the fantasy version of Twilight Imperium, and a better version to boot. I'm not sure if I agree with that sentiment since TI3 is one of my all time favorites, but that is one of them.
In terms of table time Rune deffinately hits the table more but they are both absolutely fantastic, and I can't wait to get my hands on that new expansion.