I've only watched through the first season so far and Berserker has largely been MIA (one of my minor complaints about it honestly). And I'm totally gonna check out Blade Works after.
You haven't seen the last of Berserker, fear not. Though I should warn you, this same issue will follow you into Unlimited Blade Works and be even worse. But that's what the other Stay Night routes are for.
I get that with a decently large cast some stuff is going to be on the back burner. How he and his master get handled ultimately is the more important thing.