If you disable Wayland, your system will be using the traditional display driver Xorg. For practical purposes, there is not that much difference in using Xorg instead of Wayland. Animations may be a little less smooth although this may be hardly noticeable. The most significant "regression" is that touchpad gestures are more limited.
Several tools work only with Xorg. When using Wayland, some of the functionality provided by these tools can be substituted.
xdotool only works on Xorg or, if using Wayland, with applications that run through xwayland, i.e., on an xorg instance. Some of the functionality of xdotool, in particular simulating keystrokes and mouse movements/clicks, is provided by ydotool. In fact, ydotool is more universal: it runs independently from the display manager, so can also be used with Xorg. The version of ydotool that comes with the LTS edition Ubuntu 22.04 is very outdated and does actually not work. Fortunatelly, compiling a recent version of ydotool on Ubuntu is easy.
xclip and xsel, utilities that allow to copy and paste to and from the clipboard using the command line can be replaced by wl-clipboard. There is a tool, cb, that can be used universily: it is a shell script that identifies the display driver and invokes the appropriate tools. Alternatively, the Clipboard Project is an interesting universal tool for extensive clipboard manipulation on the command line, including copying and pasting files.
wmctrl, a tool to manipulate windows, (focus, move to another workspace, maximize, ...), many of the functionality which is also provided by xdotool (but not ydotool) is more difficult to replace. In Gnome Shell, the extension Run or raise by e2rd allows to implement run or raise style shortcuts, i.e., when hitting the shortcut, an existing window is raised. If there is no existing window, the application is launched. Some extensions, like Window Calls by domandoman, Window Calls Extended by hseliger and Focused Window D-Bus by flexagoon expose dbus calls that allow to identify windows and manipulate them through the command line.
