The main reason is that it often is just much easier. Your ratio of correct clones is often very high in pGEM-T so you don't spend lots of time trying to find the right clone. In my experience I would always rather do something in 2 easy steps that I am sure will work rather than 1 more complicated procedure that is less likely to work. It is in fact often faster.

Additionally, putting your product in pGEM-T means you now have cloned into the middle of a polylinker so you have the choice of many restriction sites for subsequent cloning.

pGEM-T plasmids are optimized to be very simple to clone into - just add in your PCR product. The conjugated ligase will catalyze the reaction. No need to phosphatase treat the plasmid, no need to set up a restriction digest, etc. You can clone in 1 day (PCR in morning; set up selection plates that afternoon). This used to take a week (PCR, overnight digest, cleanup, phosphatase the vector, cleanup again, overnight ligations, etc.). Better living with science & technology!

Also, intermediate vectors like pGEM-T are an easy to make any changes to your target sequence (e.g. add a tag or change promotor). These plasmids have multi-cloning sites, known selectable markers, lots of valuable features. Easy to then digest & move to final vector.

Talk with your advisor about your specific project to plan out how to make your desired plasmid.

Good luck!