To further clarify the other answer here:
Under the current version of virtualenv, the --no-site-packages flag is the default behavior, so you don't need to specify it. However, you are overriding the default by explicitly using the --system-site-packages flag, and that's probably not what you want. The default behavior (without specifying either flag) is to create the virtual environment such that when you are using it, any Python packages installed outside the environment are not accessible. That's typically the right choice because it best isolates the virtual environment from your local computer environment. Python packages installed within the environment will not affect your local computer and vice versa.
Secondly, to use a virtual environment after it's been created, you need to navigate into the virtual environment directory and then run:
bin/activate
What this does is to configure environment variables so that Python packages and any executables in the virtual environment's bin folders will be used before those in the standard locations on your local computer. So, for example, when you type "pip", the version of pip that is inside your virtual environment will run instead of the version of pip on your local machine. This is desirable because pip inside the virtual environment will install packages inside the virtual environment.
The problem you are having is because you are running programs (like ipython) from your local machine, when you instead want to install and run copies of those programs isolated inside your virtual environment. You set this up by creating the environment (without specifying any site-packages flags if you are using the current version), running the activate script mentioned above, then running pip to install any packages you need (which will go inside the environment).