I know I'm coming into this a little late, so sorry if you've mentally got past this but... oh bugger, while it logged me out there's been a load of traffic on this, and Hes says he doesn't want a d6. Oh well, here's my hour-old and already out-of-date thoughts.
In the following "WH" generally refers to WHFB or WH40k more or less equally; if I mean 40k in particular, I'll say 40k; and D&D refers to the editions I know, from many years ago. "D&D before version numbers, when it was made by TSR" let's say.
To my mind, three of the best things about 40k are the (relatively) small scale of battles, the use of d6 and the lack of loads of tables.
I'd like to see something that combined these with a rational and consistent approach to what the numbers actually mean. So a relatively simple, fast skirmish game with logical rules that could be increased in complexity and/or detail as desired
My thoughts (many years old, and never taken beyond a certain point) would have something like "skill levels" - lvl 1 is rubbish, lvl 6 is Roland/Lancelot/Robin Hood/Darth Vader/Gandalf kinda territory. Models would have an "attack" skill and a "defence" skill. These would be modified by armour, magic, special weapons etc (btw, I would roll psionics up in the magic system - never understood why AD&D did otherwise). Also any other skills necessary - magic, flying, concealment, poison identification, navigation, repairing a spaceship etc.
No reason why these couldn't be subdivided as much as the system needs - eg, in WH, missile weapons and melee weapons are treated seperately (two "skills") but a hand weapon is a hand weapon, so needs one skill. In D&D axes, daggers, short swords, normal swords are treated differently. If you were using the system for a more RPG feel, you could be lvl1 in short-sword and axe, but lvl4 in dagger and n-sword; lvl3 in throwing daggers, lvl2 with a short-bow, etc.
So a successful "skill use roll" for a weapon would indicate that it's on its way to the intended victim, who could then defend/dodge/parry by use of a defence skill roll. I've never been convinced by the "hit-wound-armoursave" way that WH does it; nor by the "subtract target AC from 20... tell you what call it THAC0, we'll work it out from there" of D&D. Something with more complexity than D&D but less than WH (hah! who would have expected that?) seems best, or maybe I just think targets should get the chance to parry. Good old Runequest.
I quite like the rough and ready feel of WH as far as damage goes... moving between WH and D&D, a successful blow with a sword will kill a (normal) model in WH (1 wound of damage to a 1-wound Empire or IG trooper); likewise, a successful blow with a sword (d8 dam) would kill a level 1 fighter (d8hp). So "wounds" in WH are similar to levels/HD in D&D anyway: a sword in WH doesn't do less damage than a D&D sword - it just doesn't have the gradations, because in D&D it matters if you survive, in WH it matters if you're incapacitated. Conceptually at least, the number of wounds a WH character has corresponds to the number of dice a D&D player uses (incidently I also think this is a useful starting point for a 40k RPG, but that's another story)... but there would be no problem, I think, in using both systems more or less simultaneously. "1" can be absolute (as in WH currently) or it can mean 1d6 - eg, where a character with "2 wounds" is in a unit of troops with "1 wound", the damage to the troops can be thought of as "1 damage v 1 wound" like in WH, but the damage to the character can be "1d6 damage against 2d6 hit points".
Of course, there's nothing in what I've said that specifically applies to a d6 system. The numbers are kinda arbitrary, in themselves. It matters not whether Legolas has a bowskill of 5/6, or 8/10, or 85/100. It's pretty much of a muchness, just depends on how many numbers you think are necessary. I'd say few, rather than many - I like to keep things simple!
Just a few thoughts anyway...
:the taming of the cyclops:
"Well it's Forty-one Thousand Nine Hundred Sixty-nine OK -
Gotta war across the Milky Way - "
Iggius Popiscus and the Stoogii, "41,969"