If I am viewing an object (object1) and have a e-mail field in object1, which is a related field from object2, when I click the link to send e-mail... the list of available email templates comes from object2, and not from the current object (object1).
This is actually expected behavior: Related Field "borrows" UI from main field. However you can resolve this problem by constructing template field which pint to Send Email page using required parameters:
{!relatedEmail}