Model-Driven Software Engineering relies both on domain-expertise as well as software engineering expertise to fully grasp its representative power in modeling complex systems. As is typical in the development of any system, modelers face similar challenges to classic software developers, whether with general modeling concepts or specific features of existing tools such as the Eclipse Modeling Framework. In this work, we aim to understand the issues that modelers face by analyzing discussions from Eclipse’s modeling tool forums, MATLAB Central, and Stack Overflow. By performing a qualitative study using an open-coding process, we created a taxonomy of common issues faced by modelers. We considered both difficulty experienced when modeling a system and issues faced using existing modeling tools; these form the basis of our two research questions. Based on the taxonomy, we propose nine suggestions and enhancements, in three overarching groups, to improve the experience of modelers, both new to the field and those with significant experience.