Truly you are blessed, to have a 19th century baseball historian among your commenters, here to tell you that there is a lot of work yet to be done. So much so that it would probable work better for us to discuss it by email.
In the meantime, a nuance that is routinely overlooked, yet vital, is the distinction between nicknames in the sense of slangy names for teams used by journalists, and the modern nickname as trademark used for marketing. So we end up with something like this, from the discussion of the Braves: “In 1876, the team changed its name to the Red Caps, before becoming the Beaneaters from 1883-1907.” There are ample problems with that statement, starting with the detail that the team in fact never was called the “Red Caps.” I have some speculation about how that notion crept into the record, but it is a modern notion that has been repeated endlessly.
But beyond that, what do we mean by “the team changed its name”? When the Tampa Bay Devil Rays changed their name to the “Rays” they put out a press release, held a press conference, and spent time and energy chiding people who slipped up. Nothing like this happened in the 19th century. The official name of the club was the “Boston Base Ball Association.” “Red Stockings” or “Reds” was newspaper speak. For some teams, the newspaper usage was very stable. The Phillies is the classic example here. For others, the papers used various names interchangeably. At some point some researcher went back through old papers and retroactively declared which nickname was the “official” one for each year. I’m not sure when this was. I have suspicions about the Big Mac, but I don’t know. It likely was at least around that time. Whoever it was, he did a crappy job. This is where we get the absurdity of the endlessly cycling names for the Brooklyn club. Those nicknames were indeed used, but simultaneously, often is the name article. They weren’t called the “Bridegrooms” one year and the “Superbas” the next, and so on.
Official versus nickname: This too is an unduly complicated subject. Most early baseball clubs had colorful names, in the form of “Knickerbocker Base Ball Club of New York.” These were not nicknames. That was the official name. In the professional era we more often see boring official names such as “Cincinnati Base Ball Club” but there were some holdovers. “Athletic” and “Mutual” were examples. Several of the American Association clubs started out with this sort of name: “Eclipse Base Ball Club of Louisville.” They gradually switched to the boring form. The boring form opened the door for colorful nicknames. You rarely see nicknames for clubs whose official names were already more interesting. The change from nickname to trademark occurred gradually. This subject has not been robustly researched, so I can’t really pin it down. It clearly is a mid-20th century phenomenon. The Phillies’ ill-fated venture into being the “Blue Jays” is an interesting transitional case. It was like when your friend “Bob” declares that his nickname is now “Butch.” Yeah, ain’t gonna happen. When we get to the “Rays” the process is long-since completed. Some of us rolled our eyes at the change, but no one questioned the club’s standing to declare what its nickname was, but these aren’t really nicknames anymore. They are trademarks.