My experience with a spread of users who use gui launchers of this sort is that they expect exactly what Peter suggested, and find the current behavior to be obviously broken. I mention this because that feedback is uniform, to the point that people pass around their own home-grown versions of the change suggested here, and they uniformly replace the emacs gui launcher entry, rather than supplement it. Multiple times, I have seen this exchange prompted by a feelign of disbelief that emacs "still can't open new windows instead", followed by the home-grown alternatives. Another common variant is people claiming that Emacs is "incompatible" with gui launchers, with a similar "it can, but you have to fix the defaults" reply. Of course, this is all anecdotal, and it's a little old at this point as I've had very little exposure to a wide user-base in the past year-point-five, but I suggest that this is a good use of the "try it for a while and see" strategy rather than the "ultra-conservative" approach. To be more specific, it seems pretty easy to make the standard behavior the default, and include an option that retains emacs's older behavior, and see which the distros prefer. We could also try asking them directly, if we think we have enough contacts there.

Since you asked for opinions.... I suspect the issue is relatively niche. Several years ago, when I was heavily involved in supporting a large user base (MIT students, faculty, and staff), the fact that clicking the launcher-app multiple times got multiple separate emacsen was considered a bug that got reported relatively frequently. The people who wanted multiple isolated emacsen were after very specific outcomes, knew how to get there, and (for the vast majority) weren't using the gui launcher to get there. My instinct is that many people are in that same situation today, but I might be wrong about that.

Hope that helps,

~Chad