Though Qt6 is not necessary to have sorted by 24.04, I do think it is critical to get Wayland support fixed by 1.99.
Ubuntu has Wayland as the default session since 22.04, but I suspect the number of improvements to the implementation in the last two years will mean a significant increase in the number of users migrating. Fedora is even getting rid of the option of an X11 session (though keeping XWayland) completely from Fedora 40 (spring, so will include Avo 1.99), and it will likewise be gone from RHEL.
Running Avogadro works fine on a Wayland session but only if it is started from the command line, and with -platform xcb to run it with XWayland.
Unfortunately, what I imagine happens instead, and what will only happen more frequently after 24.04: a Linux user (non-technical, doesn’t know what Wayland is) who grabs Avo from the repo to check it out and starts it under Wayland is greeted with an app that just doesn’t work graphically, and will then probably be scared away for life 
So even if Wayland isn’t actually fixed, we should at least put in a temporary fix and somehow make it so that Avogadro only launches using XWayland (i.e. -platform xcb is “passed” by default).