Sentinel 2 data can be a challenge due to the amount of data. Up to 10m spatial resolution each 5 days is quite a high volume of data, depending on the extent of the region you are considering.
If this is too much for the time you have to finish your thesis you can start with a simpler problem, like using coarser resolution images (for example VIIRS has daily images at 750m and some channels at 375m).
Or you can start with regular segmentation (with month or year averages for example) and if the time allows you move for the spatiotemporal sequences. The idea is to make sure you have results along the way so even if you have no time for the big problem you can write the thesis with the results you got so far.
You may find some useful resources on the Geospatial Deep Learning resources & study group 