A boss fight in this game doesn't necessarily have to require the mothership. Early game bosses could be designed to be "picked apart" little by little by the ships the player is likely to have at that point in the game. I think at least a half dozen or so boss fights throughout the full game would be great, if they are well-designed and fun fights. The way the ships are so unique makes it kind of easy to design boss-type fights that particular ship will be good at dealing with. A good early "boss fight" might be a raid on a star system, where you have to destroy or disable defenses like maybe a minefield, a few defense satellites, and a base station (weak base). This would be easy to balance for the ships you know the player is carrying early in the game.
The mothership in SC2 is like a flying combat god. It's the fastest, most agile, most durable, has the most energy and the most powerful weapons (guided bullets!). I think the idea was that it would allow players who did not like the space combat to effectively skip it with by using the godly mothership. That might be an idea they want to carry over into the new game. It's a game design feature I call a "safety valve". In this case, people who like the space combat can use the satellite ships in fights that are hard but winnable using those ships and those who don't like the space combat but want to play this great adventure game can use the mothership to effectively skip the space combat. And the people who use the ships in normal fights would still use the mothership for the endgame boss fights that only that ship can win (although those fights might be designed to require the use of the small ships to pick apart some defenses before using the mothership).
There are a lot of interesting scenarios like a convoy raid, system defense, base defense, "juggernaut" (i.e. a massive giant super ship), starbase (i.e. massively giant super base) that might be used as a type of "boss battle" and fit into the storyline in a really cool way.