Chain Lightning & Spell Resistance

[Destil]

The most similar spell that would suggest that the chain lightning does not affect the secondary targets is Spiritual Weapon, where on a failure to overcome SR of on a creature you strike the spell simply ends, but otherwise you can later move it to attack some other creature.

I've never liked that part of spiritual weapon myself as it's not rather inconsistant with the how spell resistance works with spells like wall of fire...

 

[schnee]

... and spiritual weapon specifically described how it differed from the norm, and gave a specific game mechanic to deal with it.

Mechanically, Chain Lightning is just a targeted direct damage evocation spell that doesn't just hit an entire area (friends and foes alike). I personally wouldn't attach anything more to the 'chain' effect than 'it's special effect/fluff', because otherwise you're weakening the spell by quite a bit, especially with the number of spell resistant beasties and characters you see when it comes into play.