Another question that excludes a few examples while leaving a massive assortment of other options to choose from.
A lot of games designed as one-shots, or games that tell a single story repetitively aren't really good answers here, but it would be interesting to see systems like this challenged beyond their intended confines. I do prefer a well structured but robust system that can handle a variety of situations without breaking for this style of play.
Perhaps a better way to answer this might be to consider the games that I have successfully used for this style of play. The problem is that when I run long term games, I tend to throw away most of the system, only using the bits I need when I need them...that might be a magic system I like, or the inevitable combat mechanisms when things escalate to the point where they can't be avoided any longer. If a game can let things simmer nicely, then step up to the challenge when we need to do something funky, then that works for me.
One of the longest campaigns I've ever run was a globetrotting Werewolf the Apocalypse game...lasting through weekly sessions for almost two years... more than 20 years ago. I'd do it again, but maybe with a variety of shifter types.
Actually, now that I think about it further, I don't think the rule systems are the mediating factor for what makes a good long term play experience, I think it's more about the richness of setting. That doesn't necessarily mean high word count, but good touchstones that can prompt coherent story. The whole coherent bit is where I rule out Rifts, even if it does have a metric-buttload of sourcebooks.
I've done long form Legend of the Five Rings, and would similarly do it again because I love the depth of the setting.
I'd love to play a long term Castle Falkenstein campaign...
...actually it's been so long since I've done a long term campaign of anything, that I'd probably be willing to play almost anything in that format.