Let's look at Human baseline - WS3 BS3 S3 T3 W1 A1 I3 Ld7 Sv5+ and expected opponent MEQ.

Need a guy who fights better than the regular guardsman - say, a Stormtrooper? - A2 instead of the usual "let's make him WS4.  If he were A2, he would kill:

1/9 more GEQ per swing (to 1/3) than if he were WS4. (2/9 GEQ for WS4).
1/18 more MEQ per swing (to 1/9) if he were WS4. (1/18 MEQ for WS4 - same as WS3!)

So here we see that extra WS does not help at all if you are assigning anywere in the 2-4 range...

Need guys that are resilient to shooting but still die easily in HTH?  Raise their toughness, give them a terrible save, and feel no pain.

A Sister Repentia (and Orks even) would be a good choice for this unit - WS3 BS3 S3 T4 A1 I3 Ld7 Sv5+ and feel no pain.

A bolter would cause (2/3)(1/2)(1/2) or 1/6 wounds instead of the (2/3)(2/3)(1/2) or 4/9 wounds they sustain now.  (62% increase in survivability)

A plasma gun would cause (2/3)(5/6)(1/2) or 5/18 wounds instead of the (2/3)(5/6) or 10/18 wounds they sustain now.  (100% increase in survivability)

In HTH they would sustain (2/3)(1/2)(2/3) wounds or 2/9 which is the same as before.  As well, they would cause the same number of MEQ wounds since they WS3 vs WS4 doesn't incur a penalty.

Tougher models still would get more wounds, and monstrously tough models would get more wounds and high toughness...

They already apply these concepts to Tyranid Monstrous Creatures and Obliterators... so they just need to expand their horizons... low toughness multi-wound models already have a precident in Grotesques.

This post isn't so much for new rules, but math-hammering out the untapped potential of GWs D6 system. 

The key is balancing performance vs GEQ (T3 Sv5+) and MEQ (T4 Sv 3+). 

IMO, There really should be a more tiered system...  Example:

WS2/BS2 - Unskilled (i.e. HTH Orks at shooting, Tau at combat, Grots, Swarms)
WS3/BS3 - Average (i.e. Guard, SOB should be here too.  Guardians, DE Warriors, Necrons in Combat, Shoota Boyz)
WS4/BS4 - Skilled (i.e. MEQ, Guard HQ, Daemons, Ork HTH, Necrons in shooting)
WS5/BS5 - Very Skilled (i.e. Marine Librarians, Wyches, Aspect Warriors)
WS6 - Weaponmaster - i.e. Marine Commanders, Chaplains, Eldar Exarchs, DE Lords
WS7 - Greater Daemon
WS8 - C'Tan
WS10 - Avatar

So, the way I see this working is that the unskilled blokes (rare) have trouble hitting the skilled ones, and the average ones still hit on 4+, but every tier hits the lower tiers better, on 3+.

Extra granularity can be added to shooting by addition of more twinlinked options.

Let's take Eldar for example. 

If we made howling banshees WS5, BS3, we've increased thier MEQ/GEQ hth killing power by 33% (due to increased accuracy) and decreased overall shooting power by 25%.  This makes each banshee worth 3x 2/9 or 2/3 MEQ instead of 1/2 MEQ on the charge.  MEQs are still killing them the same at range, and strike back with the same potency...  would this offset their low toughness/armour and dangerous trek across the board?  Hard to say without playtesting.

If we make firedragons WS3 BS5, then they gain a 33% increase in MEQ/GEQ shooting killing power and 0% change in MEQ killing power (although MEQs increase their kill ratio by 33%), and a 25% decrease in GEQ HTH killing power.  This is better than increasing strength, since the prevalance of cover completely negates 50% of the effectiveness of their gun, so increased accuracy offsets this.  Granted, Firedragons don't really need boosting, but this is just an example.