There's a reason my local miniatures club is called Chicago Skirmish Wargames — it's because we like collecting small, unique groups of cool miniatures rather than vast, homogeneous armies that take eons to deploy onto the table.
As a result, we've been drawn to small, skirmish-scale rulesets for various genres. We've got fantasy covered with Song of Blades & Heroes, but sci-fi has been a bit more troublesome. The club has spent the last half a year trying out many different sci-fi rulesets, with varying degrees of success and failure. What follows here are my own thoughts (not the club's! I don't speak for everyone) about the rulesets we've sampled, what works and what doesn't.
The ground rules: we were only interested in games that encouraged us to use generic, non-brand-specific miniatures. So, Necromunda (despite being an alright game) was out.
Flying Lead — Published by Ganesha Games (the folks behind Song of Blades & Heroes) this game adds another level of complexity onto its super-simple game engine. Unfortunately, this added complexity proved to be a turnoff to me. The beauty of SBH was that it required virtually no rulebook-flipping once you understood how your warband worked. Flying Lead required considerably more cross referencing, plus we needed to use little counters or tokens to mark the condition of a particular figure (prone, fallen down, etc). I don't like tokens — they clutter up the battlefield and must be removed prior to taking glorious game photos. It's also worth noting that Flying Lead isn't really a sci-fi game — it's more of a modern combat game, with assault rifles and grenades and whatnot. Trying to graft it onto a sci-fi setting might have been our first mistake.
Wastelands — This free PDF is sort of a stripped-down RPG where you assemble a squad of dudes, trick them out with all sorts of equipment and weaponry and send them into battle against each other. The game system itself is functional and decently generic, but not particularly innovative. The best part of this game is that although it's nominally a game about post-apocalyptic battles, you can easily adapt it to a variety of sci-fi settings and genres. We've played this game quite a bit over the last year or so.
5150 — Two Hour Wargames' sci-fi title is pretty well-known, and we were excited to give it a try. As expected, the game played out differently than any other system we'd yet encountered. Basically, your little guys don't always do what you want them to do, and sometimes they flat-out disobey you. It was refreshing, in a way, and of course this sort of ruleset lends itself well to solo play. My only gripe is that 5150's point system is a bit wonky — veteran players will just tell you to play scenarios, which is all well and good, but I need a starting point of some sort.
WarEngine — This is the rules engine that powered the now-defunct game ShockForce, which was first published back in the 1990s. It's a strong, generic system that's been lovingly husbanded by its original creator, Aaron Overton, over the years. It lives on now as a thriving wiki (!) and is 100% free. Of all the games we've auditioned, this one felt the most like what I was after: a true wargame experience that took me back to the halcyon days of playing 40k in high school, but presented in a fully updated, fully supported website that's easy to navigate and totally free of charge. The game itself lets you build units from the ground up using generic statistics and game effects, which really juices my imagination. Once you've got your units built, the engine also has ways to create balanced army composition lists so you can pit your forces against your opponent.
If I had a gripe, it would be that this game seems designed for slightly larger battles than we've played lately. WarEngine games don't feel like much unless you have at least 3-4 maneuver elements (squads, characters, etc) and squads should really be 5+ models to get the full command & control stuff going. So you're looking at 20-40 models — that's almost a 40k army! Right now my club prefers games with 6-12 models per side, but I'm sure we can scale up as needed. Part of that is because we want to keep the buy-in threshold low for new players who might wander over when we're playing at our local store. "Sure, you can play, and if you want your own guys you only need to buy one box of miniatures." That sort of thing.
But still — after many months of discussing, planning and playing, I'm very excited to have found WarEngine. It's the game that I'm most excited about playing right now.