Personally, I can understand some players' frustration with the system, and the desire to reward good sportsmanship, or to reward both players in mutual agreement, rather than merely one side.
I've not commented on this for some while, but I'll take a moment to do so now: For myself, I generally offer a GG to my opponent, whether I get one back myself or not, either for an entertaining match; for showing me a strategy I mayn't have encountered before; if the final score was remarkably close; or if there was an honestly clever play, no matter if I won or lost. I try to appreciate the art of the game for what it is, although, on rare occasions, if I feel an opponent won far too easily, or if my deck wasn't capable of competing, I simply won't return a GG. As time has worn on, these latter cases have become rarer for me. I try not to let my personal frustration interfere with being a gracious sportsman, even in defeat, and I hope to see the same in others. (But, I'll not lie, I've lost plenty of times.)
Is the current GG system perfect? Likely not, especially considering the various complaints and criticisms it has drawn over the years.
So, let's consider what it's supposed to be: Ideally, GGs are voluntary tokens of appreciation, exchanged between players, thanking one another for a game they -- hopefully, both -- enjoyed. Sometimes, the enjoyment is, indeed, one-sided. Ay, Gwent can be quite frustrating, and there're often times when we mayn't feel like rewarding our opponents -- especially after a chain of defeats, facing very similar (or identical) decks. In such cases, a GG isn't compulsory. It's up the players' consciences to decide whether their foes merit thanks or not.
Does the GG system do more harm than good, though? Does it spoil the fun of the game, and foster hostility, rather than kindness? I'd say no, but for some players, the answer, apparently, is yes. While, for others, it's merely an optional means of thanking folk, and sending a wee reward.
With respect for the frustration, or dissatisfaction, with the system, I could see some possible benefit in adding a special bonus reward, in the event that both players send GGs, rather than only one. For example, an additional +2 could be added to each player's reward, if both opponents opt for a GG. This could offer an incentive to thank one another more often, or, at least, make mutually enjoyed matches feel a bit more positive.
However, I don't think that GG tokens should be denied altogether, if but one player thanks the other. That seems rather counter-productive, to my mind.