I am a freelance English editor, though I am a meteorologist and an oceanographer by training.
In English, “I” is always written in upper case; this is not because “I” am special. (Actually, “i” written in lower case may “disappear” from our fast reading—this is my explanation why “I” is always written in upper case, or did a teacher of mine tell me this?)
In research papers, sometimes we use upper case in “common names” for the same reason, to catch reader’s attention—again, my own interpretation.
Almost all oceanographers know about Ocean Station Papa (OSP or Sta. P), which is located at 50°N, 145°W. (If you don’t, just google it.) Note the upper case in this station name: Station P.
Example: We collected data from three stations in the South China Sea, which are marked in Fig. 1 as Stations A, B, and C.
Note that upper case is used for “Stations A, B, and C” in the above sentence.
How important this rule is? Well, I can say for sure that the journal editor will NOT reject your paper for this reason alone, but you should try to follow this good rule. Say, you define three phases for a life cycle of a storm, then you would say "Phase 2 is the focus of this study, because we only have limited data for Phases 1 and 3."