Ok, since the other thread was generating some questions, I decided to try a Stealth Rock modifier.
I ran some simple numbers for a Stealth Rock damage adjusted value. I deducted 25% for a 2x weakness and 50% for a 4x weakness. This is what resulted from the Pokemon I've already done:
Pokemon, Original Value->New Value
Abomasnow, 12->9
Aerodactyl, 23->17
Altaria, 16->12
Arcanine, 13->10
Araidos, 6->5
Armaldo, 9->7
Articuno, 18->9
Beautifly, 10->5
Beedrill, 9->7
Butterfree, 10->5
Charizard, 19->10
Chatot, 12->9
Cloyster, 12->9
Crobat, 21->16
Dragonite, 19->14
Drifblim, 17->13
Farfetch'd, 8->6
Flareon, 10->8
Froslass, 17->13
Glaceon, 9->7
Glalie, 10->8
Gyrados, 15->11
Honchkrow, 16->12
Houndoom, 17->13
Moltres, 18->9
Mothim, 11->6
Ninetales, 12->9
Ninjask, 17->9
Pidgeot, 13->10
Salamence, 22->17
Scyther, 15->8
Staraptor, 14->11
Swellow, 16->12
Togekiss, 19->14
Walrein, 14->11
Weavile, 19->14
Xatu, 16->12
Yanmega, 17->13
Zapdos, 19->14
Does any of that sound reasonable? Did that kind of change solve some of the anomalies that are present?
Just an inital thought. The deduction might be too much, but I figured I'd ask for opinions.