Something that bugs me about the introduction of Rime to the Myst canon (recall that although the Stranger visits Rime before Riven in the canon, Rime was added in realMyst in 2000, after the release of Riven in 1997). While I love the addition of the Rime Age and the way it connects Myst to the Riven story and the greater D'ni story, it seems to undermine a lot of Atrus' motivation in Riven.
From Atrus' Rime journal on Myst Island:
Within me is an urging to take the chance and return to D'ni to find these survivors and properly rebuild our city. However, I can do nothing until I am certain of the fate of my father. If my plan failed, if I missed a single Book when attempting to trap him on Riven, then he has been free all along. If that is true then all that stands between him and the Ages I have now written is the link from D'ni to Myst.
We know that Atrus and Catherine succeeded at viewing Riven through the Rime crystal viewer, long before Catherine was trapped on Riven and Atrus was trapped on K'veer.
And from Atrus' Riven journal (87.7.16, three days after the Stranger fixed Atrus' Myst book):
The deteriorated state of the Gateway Image makes the use of a visual signal impossible, but the picture remains a reliable indicator of Riven's condition nonetheless: by measuring and interpreting variations in the noise patterns, I am still able to observe basic changes that occur in the Age - even though I cannot see them. The problem is that my instruments can only detect changes that occur on a fundamental level, and it seems unlikely that an individual could effect such an elementary change from within an Age.
Why couldn't Atrus have simply gone to Rime to view Riven through the crystal viewer? Then he could have arranged a much simpler visual signal (a hearty thumbs up?) for the Stranger to communicate that the mission was accomplished, avoiding the need to trigger the destruction of the Age in order to signal Atrus.
I suppose Riven would still have been destroyed eventually, so it's just a minor plot hole, but as I said, it kind of bugs me that realMyst kind of retroactively inserted this plot hole into Riven.
PS. I got easy access to journal quotes thanks to Journals of Myst, a site that lets you browse all journals from the Myst series and Uru, and has been kept active for over a decade now!