Relying on small variations of the same symbol to express different sounds is fundamentally bad design, which makes reading strenuous
especially for non-native speakers.
A native user of a writing system doesn’t have a problem understanding it and doesn’t feel any “imperfections” of it.
When it comes to non-native speakers or writing system users, Latin is the most common alphabet in the world and Cyrillic is actually very confusing for Latin users because of many false friends. Your argument is invalid.