what seperates jm from cs is about 40 more weapons and a greater incline towards realism. the reason a lot of the weapons are the same is two-fold: 1) most of the similar weapons are very common in the world, or have a reputation for being good weapons (mp5, ak-47, barretta 92fs) 2) the less common weapons are renowned for their traits or the group that uses them and/or bring a different set of stats to the gameplay (bizon, svd, rpk-74).
another thing that seperates jm from cs is the afformentioned ANGEL stats system. as far as i know, no fps in history has ever even attempted something like this. not to mention the ability to upgrade your weapons with LAMs, scopes, bayonets, grenade launchers, and an assortment of other attatchments.
and i agree, theres a serious lack of originality in the mod scene and in the game industry, but fps's are (relatively) easy, and theres still room for innovation.