There are some points to consider, regarding this.

1. Think about the person slicing an onion, tears roll down through eyes. It's due to the presence of sulphur, and human body naturally is not acquainted with such chemicals, so it resists by activating tear gland. Now, you are eating the whole thing, that's too much for our body to bear.
2. It's also due to the strong smell, which is a sign of impurity and non-serenity, and people finally end up hating this smell. Those who eat already know.
3. People constantly argue, that they have a good medicinal value. But when you are talking about medicine, you must also know that medicines are taken in a limited quantity and we usually do not make chutneys and sabjis of our medicines.
4. If you are a Hindu, or know something about Hindus, you may know that, we do not offer Onion & Garlic to our deities, neither you will be served with them at any temples.
5. They are considered as Tamsik food, which arouse qualities like anger, laziness, and divert us from the correct path of spiritual knowledge.