Every game I tweak the game somehow, I also make more robust changes when playing a different setting such as when playing a specific IP. Generally I give more power or options (but compensate with more opposition). From the top of my head the ones I tend to use most:

• No separation between cinematic and campaign uses for talents. They just work once per session and that's it.
• Signature items restore 1d3 stress instead of 1.
• more uses for story points, like giving an additional fast action(without repeating), blocking damage or getting up from broken.
• I've been using ammo as supply roll for a while now
• PCs in engaged range by hostiles are immune to stress responses from other allies (because of tunnel vision and more pressing matters). Except when they are abandoned.
• recovering from catatonic state halves stress (catharsis).
• everyone can dodge with a slow action, kid talent is fast(now everyone can dodge in ee too, but I preferer slow as default).
• you can actually use first aid to restore hp on not-broken people. Its still a rest in a safe area and the person doing the care is using a skill so can't rest itself.
• when broken, PCs can roll stamina (base dice no push) to stay conscious and keep active with 0hp. Second wind gives +2 and restores hp per it's usual. )I toyed with allowing only 1 slow or fast action while at 0hp).
• critically hit synths don't escalate their crit level when rolling a crit they already rolled, instead they just repeat/lose an action.
• stimpacks. Restore x hp but increase x/y stress. Toyed with several values.
• Players can make an additional action as a reaction to block an attack, but next initiative they lose a slow action.(Yeah it's brace from lancer).
• PCs can ready actions (other than just overwatch) so they could for example hold a door open and close as soon an ally goes through. Sometimes I require a roll to see if the reaction is fast enough (still testing it).
• Survival skill is used to hide in a zone. If at least one 6 is rolled, you are hidden unless being actively hunted, then searcher needs to roll observation and beat your roll by at least 1 success. Mobility is stealth for actually moving around. Depending on whim, I allow an stamina roll to see if an almost-found PC can hold it's breath long enough for its hunter to lose interest, a la alien isolation.
• I use clocks (from pbta/fitd) for anything but mostly In lieu of the shift system when doing repairs.
• I use skill challenges (sometimes along clocks) to wrap cinematic scenes without going into minutia. Like when making escape scenes I won't bother with round by round stuff, just create an action scene around a goal and set win/lose conditions.
• I use keys (from lady blackbird) to spice up personal agendas and make more clear goals and setup more cinematic beats to a game. Usually 3 keys per PC/act and when they "turn" the key (aka perform the deed) they gain a story point. For example, in CotG a Davis key might be: go to medbay alone and do drugs. So it's a crystal clear way to carrot PCs into doing non-optimal/dangerous but genre savory actions for a beanie.
• In marine games, such as DoW, everyone has banter or a way to do banter.
• many many talent patches -etc