Addressing the recent trend of the massive demand for resources and ubiquitous use for all citizens has led to the conceptualization of technologies such as the Internet of Things (IoT) and smart cities. Ubiquitous IoT connectivity can be achieved to serve both urban and underserved remote areas such as rural communities by deploying 5G mobile networks with Low Power Wide Area Network (LPWAN). The current architectures will not offer flexible connectivity to many IoT applications due to high service demand, data exchange, emerging technologies, and security challenges. Hence, this paper explores various architectures that consider a hybrid 5G-LPWAN-IoT and Smart Cities. This includes security challenges as well as endogenous security and solutions in 5G and LPWAN-IoT. The slicing of virtual networks using software-defined network (SDN)/network function virtualization (NFV) based on the different quality of service (QoS) to satisfy different services and quality of experience (QoE) is presented. Also, a strategy that considers the implementation of 5G jointly with Weightless-N (TVWS) technologies to reduce the cell edge interference is considered. Discussions on the need for ubiquity connectivity leveraging 5G and LPWAN-IoT are presented. In addition, future research directions are presented, including a unified 5G network and LPWAN-IoT architecture that will holistically support integration with emerging technologies and endogenous security for improved/secured smart cities and remote areas IoT applications. Finally, the use of LPWAN jointly with low earth orbit (LEO) satellites for ubiquitous IoT connectivity is advocated in this paper.