For Inquisitor style games with a handful of figures on each side, I've seen people use the Pulp Alley and 7TV rules. Both cover larger than life characters with special powers or abilities pretty well, and both are designed for playing differnet genres. You can probably knock together character profiles with a
40K feel from the rules as they stand.
For bigger games, Stargrunt II and Tomorrow's War are fine systems are about the right scale but very realistic - deadly, and you will spend time hauling screaming casualties and prisoners off the board... You could certainly get some interesting rules mechanics from them.
The
RPG Savage Worlds works well at the skirmish scale - again it's a game that is designed for multiple genres, has grunts and heroes, and has a system of "Powers" that covers everything from psykers to kitbashing mad inventions. Core rules are free from Pinnacle's website, fast to play and streamlined, and there's a free download called Showdown which streamlines the game even further for minis (so powers activate on a dice roll - no tracking power points) .
There's a setting book for Savage Worlds called Necropolis 2350, which is set at the time of Humanity's last stand against extra-dimensional undead/demons. It's basically
40k with the serial numbers filed off, and covers a ton of weapons, armour and vehicles.
Bolt Action is about the scale you're looking for, but doesn't really cover armour well. There's a little fan supplement called Bolter Action that gives broad rules, or you could look at Beyond the Gates of Antares which is a more detailed version of the same system.
Second Edition
40k?
I'd avoid the
40k RPGs - far too detailed and the rules systems are not particularly great.