Many of my previous house rules were actually adopted into the final rules (or made irrelevant by changes elsewhere), so I figured I'd post a little update on some things I've been doing and have been working for me since the 1.0 release.
Lifepath Chargen - I always let my players roll 2d6 for any specialties, etc that they might pick up and choose which one they like. I'm just nice that way.
NPCs - I rarely use many of the simplified rules for NPC coolness under fire, reloading, etc. I do try to have my NPCs act in buddy pairs, if there's more than a few of them. I sometimes use my NPC wounds table to quickly resolve hits; it saves a bit of time in bigger fights and also helps generate morale/motivation outcomes, if I haven't come up with break points or something in advance. I think I'd like to do a version of this that directly incorporates CUF into the roll, rather than requiring another roll entirely. Right now you do still need to do 3 rolls if you care about CUF and if you care about hit location... so it's actually adding a roll at the benefit of eliminating record-keeping for hit points. Not ideal but it does help in some circumstances with fodder NPCs.
Night Vision - I find the ranges and rules for nightvision to be kind of silly. I have a pretty significant amount of experience patrolling with NODs and it just doesn't feel right. My rule instead (easily implemented in Foundry, my VTT) is that any form of NODs give you a bright vision range and a dim vision range. Within the first, you can see well, make out most details, etc. Within the second, you can see, but you can't make out details (so for instance you really can't tell if that guy has an AK or a M16). All firing penalties still apply. You get a +2 to Recon rolls relating to ambushes and encounter ranges.
MGs - machine guns are in kind of a bad spot in the rules as it is. Other than holding a lot of ammo, they offer no real benefit and have some significant drawbacks. This wasn't much of a factor until I got a character who really wanted to be a machine gunner. So. RAW give MGs significant penalties unless they are deployed using the bipod/tripod/something. Fine, makes sense. But the rules don't give them any benefits! What are the real-world benefits of MGs? They put out a lot of fire, and cause a lot of suppression. So my current experimental house-rule to give MGs a bit of love is this: all RAW still apply, but when deployed on the bipod, they get to re-roll up to 2 ammo dice on each attack. Two obvious caveats about this: 1) yeah, it also increases the chances of a mishap or jam. I think I'm relatively ok with this... many MGs are quite notorious for jamming. 2) it adds another roll. I'm not as okay with this. An alternate I may try is that a deployed MG may convert any two 5s rolled into a 6, for instance. This would come up pretty rarely, but I'm just looking for a little boost here. I also rule that the additional hits must be handled as separate hits (to the same or different target), not as increased damage.
Better Practices (these aren't really rules, just observations I've had in terms of running the game)
- zoom in and out of the RAW. Sometimes, the constant threat of encounters and the use of shift-by-shift travel rules is exactly what is needed to keep the tension up or generate some excitement. Other times, the players are really just pursuing a major story beat, and it's best to stay out of their way as much as possible so that good stuff can happen! In this case, I still check for encounters, but if it's not something I can think of a straightforward way to tie to the big-picture story or use to reveal a clue, I skip it.
- use the "Solo" rules! I personally find this section invaluable even for non-solo play. Especially when it comes to the above, and generating encounters that lead somewhere and keep the story moving, I find it generates much better results mostly because it makes me do my own interpretation to develop encounters. I also use Mythic GME for this and for many other things.
- likewise with the "mood elements" included in the book. Some of these are quite nice for painting a picture, when you don't want or need a full encounter. But players have a tendency to treat everything as a clue, as a significant threat, or as something that must be followed up on. Be careful including these if you don't want to spend half an hour to an hour carefully exploring it, or have it misinterpreted as having some undue importance in the world.
- I use Angry GM's Tension Dice whenever and wherever I can. It's a really nice, straightforward system for communicating a looming sense of threat to the PCs, especially when they're doing something like infiltrating an enemy camp, etc!
There are more house rules I will probably eventually implement. A skill change to break up Recon, Persuasion, and maybe Tech is high up there, but it's kind of a big hassle when running with existing characters. As in the recent Initiative discussion, I'm evaluating some big changes there as well, not sure how I want to play it yet really though. I'm also pondering a rule for automatic successes for highly skilled characters, in some circumstances (mostly travel-related). The dice come out really swingy sometimes in a way that is hard to justify for highly experienced survivors.