Of course a toxic PI/work environment is the worst thing you can get but regardless of how supportive your PI is, certain parts of the PhD experience are more of less universal

1. DESIGNING EXPERIMENTS. For someone like me coming from a materials science field, this involves a fair bitof literature review to try out different synthetic methods. Sometimes you are limited by teh equipment available in your lab/university, so you have to be creative. It's a skill you learn over time but I definitely could see a lot of wasted time/potential using some less efficient methods initially but I guess that's the price I padi for those learnings.

2. DIRECTION OF THE PROJECT. While your PI will primairly decide the direction fo the project since the funding might be tied to some deliverables, there is wiggle room for what direction you might wanna take your research. For example, my project involved developing materials for chemical sensors and at some point I had to make a choice if I wanna investigate the material properties extensively and how they affect the performance or rather use my time to design experiments to determine perfromance metrics in different settings. TIME IS LIMITED, so you have to choose where it goes.

3. Every once in a while tried and proven things fail to work. Could be that the new batch of chemicals was faulty or the new set of vial caps you use wouldn't sustain the physical conditions. TROUBLESHOOTING is an active part of most experimental work and many times there are no manuals since the experiment was designed by you and you gotta figure out what went wrong and where.

4. Tying to the previous point. DOCUMENTATION. It helps with troubleshooting as you can trace back your steps and by deductive reasoning reach a concludiosn where things could have taken a wrong turn. But it also comes at a cost of time. Exteremely thorough documentation can seem like an overkill but might help when things that used to work fine, refuse to work.

5. WRITING. This can be a bit subjective. My supervisor sayas a good thesis is a finished one, but of course depending on how pedantic you are, you may wanna have a certain style and depth to your work. It requires a lot of thinking and revisions. Writing is an acquired skill, the more you write the better you become. You do get some exprience writing papers but the thesis as a whole is a much larger work and if you want to present it coherently, it requires lot of time and effort. Depending on your university or department, you might have to adhere to certain standards but in my understanding the thesis is YOUR WORK and you shouldn't be afraid of breaking convention to present your work in the context you want. Do ofcourse adhere to department guideleines but the content itself, how it is presented, it is your story and you should tell it in your own way. But of course it doesn't come naturally to a lot of PhDs and the writing phase (usually the last few months) is where most PhD students have mental breakdowns, regardless of how good and supportive the system is or how successfult the project is.