I've never played any version of 40K other than the first edition. That was a lot of fun at the time, but it's not a great ruleset in my opinion. I bought the rulebook second-hand fairly recently, out of pure nostalgia. And it's full of great things: the plot generators, the DIY aesthetic, the background and all those evocative Ian Miller and John Blanche illustrations.
At the weekend, I looked through it and thought about running the farm scenario for my son and friends (I've been painting up some of
these chaps recently). But re-familiarising myself with the mechanics, I was reminded of just how clunky the gameplay seems now. "I go, you go" is hugely outdated, the profiles are so stat-heavy, and the combat system is really laborious. I don't know, but I gather that later editions didn't really fix these problems.
My impression, from a friend who plays the current iteration, is that the background really just carries the rules for people like him, who actually prefer painting, converting and fluff to the gameplay; as he puts it, "I play so rarely that I just want to see lots of spectacular models moving around the table".
I'd recommend a couple of systems for small-scale skirmishes with the 40K background. First, Rogue Planet. We've had great fun playing this recently: it's got lots of innovative, state-of-the-art mechanics and is
very fast-playing. It's perfect for 40K, in that it has rules for power fists, chainswords and the like. There are some suggestions from the author for statting up space marines and the like in the discussions
here. There's a huge amount of fun to be had with this, from using power fists to throw opponents into dangerous terrain to "bug-hunting" against seemingly impossible odds by using the group rules. The pawn rules (where leaders get followers that are represented by miniatures but just add abilities to the leader and act as hit points for them) are great for 40K, given the models available (servo-skulls, gretchin carrying their masters' weapons, standard-bearers, etc.). It's both a high-tech system that models suppression and overwatch well and a fantasy system in which power swords and shields make sense.
The other thing I'd recommend is one of the Ganesha systems. Mutants and Death Ray Guns is a lot of fun, and then there's Flying Lead, which is adds more realism. Both have the huge advantage of working well with more than two players. So, if you want to play multi-player games with four to six miniatures a side, one of those would work really well. The new supplement for MDRG adds reactions, which break up the turn sequence a bit more; those are designed for two-player games, but Andrea, the author, has published a fix for multiplayer games on the Song of Blades and Heroes Yahoo group (essentially, players draw cards to determine who is allowed to use reactions in a given player's turn). And Osprey are bringing out Andrea's Rogue Stars in December, which is a different system but is eagerly anticipated.
All of these rulesets are really cheap, well tested and well thought out.