The primary difference between incorporating a business at the provincial level versus across Canada is name protection, annual filings, name selection, business reach and costs. Incorporating on a provincial level means that the name of the corporation is protected within that area/province.
The rules are not as strict in terms of the business name uniqueness, so long as there are no other matches similar to the choice. However, this process means that your name is not protected outside of the filing province if you chose to ultimately expand it to other territories.
Registering your business at the provincial level only enables you to conduct business there and you must also maintain a local office there. However, this does not stop you from doing business with companies within other provinces. You are also responsible for filing an annual corporate return with the provincial government within sixty days of the anniversary date of the incorporation
Federal incorporation, however, is different because it requires stricter naming selection that also gives you greater protection. A report will identify the database of corporate names to determine if your name is distinct enough from any other registered name in Canada.