Greybirds on the money there with the WEG game,
but if you want a more "modern" hybrid,
try this;
port the parts you want (like force powers and squad construction)
into the system you love (W40K or 'Gobs', etc).
I find that you can already play star wars minis as-is as though it were a tabletop. Just replace the word squares with inches (or x 2 for cms, whatever really). Force powers work the same, you dont need the maps and youre on your way
If you want, you can make a more complete hybrid using the custom rules from W40K
My local RPG group use the rules for super heavy fliers for the vehicles; just change the names up a bit.
Space marines become Clone/Storm troopers.
Jedi are psykers (but they use WotC SWM rules for the powers)
Fringe are mercenaries/dogs of war
Choose the parts out of the codex's you think best describe the type of battle you envisage.
Its best if you and your opponent sit down and nut it all out before playing, maybe start with a SW40K in 40mins adaption? and see how it goes from there?
IMPORTANT --- dont mix the two points-systems! Choose either GW points or WotC points systems and stick to them. GW points work out cheaper in really big battles vs WotC points.
example: Clone trooper (spacemarine) 15pts GW
Clone Trooper 9 pts WotC.
I also think in terms of mechanics, if you try importing CE's or Opportunist/Attacks of Opportunity... it gets a little messy.
Turn structure is very important then. Same goes for initiative (for abilities like recon and reserves).
Hopefully thats some food for thought anyhow
Im still ironing out some of the kinks in our houserule at my local gaming group; some of the alien encounters dont go too well (too much ork-iness for ithorians/nautolans/rodians for my liking...)
Look forward to seeing what you come up with, and battle plans etc with your hybrid rules.
Maybe checkout Warseer and Dakka Dakka as well, there were some good discussions over on them...