This all depends on what "level" you want the feature to take effect.
You might have some success, for example, by generating your own keyboard table (man keyboard to start down that particular rabbit hole) that swaps the functionality of arrow and ctrl+arrow to the point that most software will think you have pressed ctrl+arrow when pressing the arrow and vice versa.
At the other end of the scale, a window manager might be able to override one or the other, or possibly both, depending on available features.
For example, in Cinnamon (and possibly other GNOME variants) it's possible to set up triggers for most keypress combinations (occasionally single keys too), capturing and processing before being passed to any software that might be running. Triggers can call commands like xdotool or anything else really. You may need to throw a sleep 0.5 before the call to xdotool in the script / command-line to allow control to switch back to the running software. YMMV.
(If you're really clever, you could assign a keypress that shuffles some symbolic links around, modifies a configuration, or some such, effectively allowing a feature to be toggled without having to modify the keypresses. Exercise for the reader, etc.)