Prior to the COVID-19 pandemic, Computer Science and STEM-related fields were among the most resistant to online courses. This is because of a perception of the need for more hands-on instruction with labs, clinicals, field studies, etc. Additionally, many STEM students had perceptions based on limited experience of an online STEM course. Therefore, investigating how the pandemic affected students' perceptions over time is very important. This study investigates the evolution of student perceptions after one and a half years relative to synchronous courses, asynchronous courses, overall satisfaction with online courses, and lab and project-based courses. Our analysis is based on two surveys conducted in the Spring 2020 and Spring 2021 terms, i.e., the first and last semesters that the university converted to a fully online mode. We hypothesize why there were significant empirical shifts in some areas and not in others, and make recommendations based on the qualitative student responses relative to best, acceptable, and poor practices. Our main findings include: (1) Students' perceptions of online classes have improved but are far from equivalent for a lot of the students. (2) Lab resources have improved a great deal, but lab experiences have only improved modestly. (3) Although students' preference between synchronous and asynchronous online modalities were evenly divided, it did not significantly affect students' perception of their learning experience. (4) Grading policies have left many students anxious and confused. Recommendations are provided at the end of the paper.