What about changing the signature of the method to
public IQueryable<TEntity> GetAllIncluding(IEnumerable<Expression<Func<TEntity, object>>> includeProperties)
defining your conditional logic elsewhere
var args = new List<Expression<Func<TEntity, object>>>();
if (useEmailNotices)
args.Add(u => u.EmailNotices);
and then simply calling the method like
IQueryable<User> users = repo.GetAllIncluding(args);