All RPGs in the last 20 years or so have optional rules and expect some levels of house rules. I think you are blowing this out of proportion.
The issues is not optional rules or house rules perse.
The issues are optional rules dressed as suggested norms with no true alternatives suggested.
An optional rule is just normally something to change the way the game is played in a flavor or tactical sense.
Such as RG1-RG5 in "Run and Gun", or the expanded lifestyle rules in "Run Faster"
And are not presented as this is how we set it up in the base rules, but you don't have to use it.
House rules are fine if they are imposed to bring a working game inline with the tables preference in play-style.
But I can not support the idea that a company should count on players to create house rules to fix issues with their game.
Just to be clear CGL has never made this statement so I will give them the benefit of the doubt that this is not their official response.
But This is why I will not support the idea that if a game mechanic is perceived to be broken by a large group of players the answer is just to house rule it.
To me this is a lazy answer to this issues, and promotes an air of non-concern or indifferent for the players bases prescription of the game, be it a small number or a large number which is hard to determine from just a forum or a few review site reviews. On both sides of this you have to remember that most posters here come from groups of players (The campaigning group) that can range from just the reader to 6-8 people in number. so to dismiss every comment as just a squeaky wheel is wrong and can be devastating to a game (D&D 4th anyone).
The point is if as MC stated, their are whole pages of players complaining about the system("It sucks") as it stands, and only a few are praising it, there may be a issues there that "Just House Rule it" will not solve.
I have started this ad nauseum, but I don't think 6th is a horrible attempt at a Shadowrun game system.
I just feel that it has issues about where the priorities are with the mechanics.
Edge could be a wonderful addition to the game if it was not the core mechanic that it's presented as.
I'm not even say it should be only an optional rule, but I don't logically see it as a complete replacement for the modifiers system or portraying the effects of armor, etc.
It is a bonus mechanic nothing more, so it fails massively as a modifier mechanic which needs to work effective both way and not just in the positive.
Just to be clear "0" is not an effective negative, nor is the defender gets a bonus and you don't when the bonus by itself (without existing edge) Doesn't come close to emulating the penalties that it is replacing.