I'm alittle tired so this might be idiotic, but I prefer the "in addition to" saves of the advanced rules. However i think they do make for nasty situations (ala Terminators) so i have tried to think of a way to balance things. Its simple, so only a brief explanation is needed.
Targets in Cover: When a unit fires, the number of hits show how many where able to fire successfully in the vacinity of the Target. When such a target is within cover, there is a risk even these shots might strike a wall or other item.
All successful hits are re-rolled, needing a roll of 6 minus the cover value to actually strike the target.
Examples for comparison...10 Tau firing at Space Marines in 4+ cover.
Current = 5 hit, 3.4 wound, 1.1 Kill.
Advanced 40k = 5 hit, 3.4 wound, 1.7 after cover saves, 0.6 Kills.
My way = 5 hit, 4.2 pass cover, 2.7 wound, 0.9 dead.
Theres only a 0.2 discrepancy between the current and my way changes, while advanced gives a rather large 0.5 shift.
Personally for me the problem is not the actual cover save, but the fact its taken as a cover save AFTER wounds when in reality shots would not wound first, then bounce off cover. Instead i've tried to factor cover into the number of shots fired at a squad, before wounds....resulting in a small, but valuable reduction in Kills.
The 6 rather than 7 is just to make cover useful while not being a key game factor, even though it negates 5+ cover (using a basic 7- to allow 5+ saves would result in a 0.7-8 result.).
Anyway, something to ponder over.