During the campaign I went from sniper rifle to EM Rifle, and didn't really notice a loss of performance. At least up until the Encased Plasma Ammo, where I think the damage output really out classes the EM Rifle (not just the light class extra TU ie double shot, as much as there aren't any resistances or armour values to detract from it) .
I don't think the game takes advantage of through wall RF, If I remember Telok says it'll shoot through another Alien, but I'm not sure this applies to walls (which will break the LOF and consequently the RF cycle?).
Either or, seems rookies with the Encased Plasma Ammo, have a better mission to kills ratio then the my more experienced soldiers with EM's. Of course being rookies, (less then 10 missions) I can't say they are REALLY out performing..
I should say, I really like the accuracy of the EM Rifle, and take a lot of long distance shots on my turn, but don't try to RF with them which limits their viability.