Then we would have never developed (extremely effective) vaccines, antibiotics, antifungals, death rates from disease would still be near to what they were during the middle ages, smallpox and rinderpest wouldn't be eradicated, millions of children in first world countries would be stricken with polio, measles, mumps, rubella, and a hundred other terrible, scarring, often-fatal illnesses every year, we wouldn't be encountering increasing antibiotic resistance (because antibiotics wouldn't exist), and a great deal of modern medicine would be an utter sham.
The fact is that the evidence supporting the germ theory of disease is absolutely overwhelming. No, it's beyond overwhelming. The amount of evidence supporting it is so great that I'm not sure there's a word or phrase that can really describe just how well supported the theory is. We have detailed understandings of how almost all forms of infectious diseases (bacteria, viruses, fungi, etc) function, from the molecular machinery which reads DNA and assembles proteins all the way up to the spread of entire pandemics. That's not to say we know everything, merely that we know so much about disease that the idea that germ theory is substantially incorrect is like saying that we don't understand how cars work. While we are still making improvements to the automobile, no one in their right mind could claim that we don't understand how cars work.
I know of no inadequacy of germ theory. It is just extremely difficult to counteract or outdo the pressure to adapt that evolution places on populations of germs.