Now, I have mixed opinions with the Boss store if it ever gets implemented.
I also believe that the normals' shop needs to no longer exist as it is now. If it were changed, preventing players from buying minibosses to begin with and instead incorporating it into normal classes somehow, that it would be better. For example, as a rocketman you have a chance to become Master Chief, overweight could become Juggernaut, etc. At that point we would have to make something up for the rest of the classes, but it probably wouldn't be too hard in the long run. But back to the point, I do believe we should throw the shop out in exchange for something else. Too often can someone use a miniboss and be boss the next round, every couple of rounds on a low playercount time, which lessens the fun and drives players away.
Tl;dr, Minibosses and the idea of boss upgrades are used to make the other teams' experience an unhappy one. I advise to remove minibosses and rework them into the game with other methods. We could still keep the boss upgrades, for instance if too many minibosses are in a round, the current boss will get the upgrade. So while gameplay changes a bit, it still attempts to make it fair on both teams without players trying to ruin an experience for others.
I like the idea that is stated in the second paragraph, where the more minibosses there are in the round, the more buffs/upgrades the bosses get. HOWEVER, I do not like the idea of damage boosts, or health boosts. I feel like upgrades for bosses should be somewhat specific. Example: If (blank) amount of minibosses are chosen, Dark Samus gets a buff to her recharge, making her recharge faster. Something along the lines of that. Passive abilities that aren't super powerful for the boss, but something that could help it in several situations. I can dump ideas for passive abilities for the bosses, if needed.
Another thing, if that idea is implemented, is a miniboss "point" counter. Now, what do I mean by this. Well, there are a few dominant minibosses. Master Chief, Jug, and Decker are the ones I mostly see used. Now, if the upgrades for the boss is determined by the amount of minibosses used, then this could be a problem. The Vagineer and Christian Brutal Sniper, while still useful, do not have the damage potential that the other classes do (in my opinion anyway). For the boss to get an upgrade because two support minibosses were chosen could be problematic. So, each miniboss could be given a point value. Example: Dark Samus gets a slow passive recharge for her energy meter if the Miniboss counter reaches (blank). Because Jug is worth (blank), and Doctor Oktoberfest is worth (blank), this limit was exceeded, giving Dark Samus this upgrade. Of course, if the counter is lower, they wouldn't get said upgrade. I have absolutely no idea if such an idea is possible or not, however, but I feel as though such a system would help balancing the boss upgrade idea a bit.