While I listed two, I mean two major issues. If I have to make minor rules calls or change a few numbers here and there, that's fine. If I have to make major tweaks, 2 is my limit on those.
Savage Worlds, 2d20, and YZE, I've not found a need to do house-rules for play, per se. I've integrated bits from multiple worldbooks in Savage Worlds.
Prime Directive, my house rules were simply listing the options in use and adding some additional equipment, and a couple canonical races not discussed in the SFU.
LUG Trek, I simply reverse the roles of attributes and skills in the dice mechanics. That solved most of my issues in play with it. It's issues in play. The other change I had to make was jus tmaking specialties always X over the base skill, rather than the taken at fixed level, and if not raised before the base skill is equal, lost. There were a number of minor issues that weren't huge, and I, at the time, preferred the Star Fleet Universe (of SFB and Prime Directive) to the (then) Canon Trek Universe (TOS, TNG, DS9, Voyager)
If there are large numbers of minor issues, They can add up to "Not again."