Multiplayer seems more of a race to the Merc Survey ships at the beginning of the game, especially the one that provides 100 credits per anomaly.  Otherwise it isn't too bad at least it hasn't for the multiplayer games I've been a part of.

Suggestions that I'd and some have suggested to Mercenaries are the following...

• Cool down for Multiplayer games, allow 1 Mercenary ship to be purchased every 5 turns (which resets if other human players have purchased one each in that time frame).
• Have cost of Mercenary ships scale for players strength (both overall and economy).  This will help narrow the field of making the stronger, stronger.  Instead one could say the Mercenaries aren't just in it for making more money (credits) but, are there to secretly destabilize the galaxy.  You could go one step further and give weaker players a better rate per strength/credits compared to stronger players.
• Have the number of Mercenaries scale per map size.  Maybe cut down on small 2 player games to a total of 12 Mercenaries available and at large 100 player games actually add to the existing pool up to 144 Mercenaries per game, yes this still gives the player a rate of 1:6 in small games but a rate of almost 2:3 in larger games.
• All Mercenary ships to be upgraded (for cost, and you could do this by the same scale as above).  Have to contact Bazaar and may cost additional resources as well.  This would help prevent the Bazaar from becoming useless mid game.  (Yes, I say mid game because on larger games a player can unlock all of them by turn 100 even on very slow game pace/tech rates).
• Improve AI use of Mercenaries.  Right now even Godlike AI in an 86 player game, have only purchased about 6 of the 36 available in the game, I purchased the rest.  Huge advantage for the human player.
• Add new Mercenary ships to be added to the pool once a Mercenary ship is used/destroyed.
• Have some Mercenary ships that are tied to ideology points based on choices made with it not, just for winning battles.  (benevolent and pragmatic)
• Here are more suggestions for Mercenary ship ideas not present in game or only one in game. (Where some specialities have more than one).
• More special ships that convert dead planets to class x planets (right now only one where as there are colony ships available in the last two groups and by then most players have colonized planets.)
• Colonizing ships that can colonize special worlds such as radioactive/toxic (being that players with the adaptable or aquatic traits already can colonize level 1 extreme worlds).
• Mercenary that can flip star bases in area of effect, this one would have larger area of effect than normal as you would have to build a certain distance away to begin with.  (Already have one that can flip planets.)
• Mercenary that can flip ships in area of effect.
• Mercenary that can find "hidden artifacts" build anywhere and will have appear precursor relics with in area of effect anywhere from 1-3 random.
• Mercenary that can find "hidden artifacts" build anywhere and will have a high rate of anomalies appear in area of effect (larger area of effect.)
• Mercenary that can make star system appear out of no where with anywhere from 1-4 habitable planets in system.  (less war like more peaceful like).
• Mercenary that can make a planet appear from no where around star with in area of effect.
• Mercenary that can build star base and then provide x credits per turn based on # of other player star bases in area of effect.
• Mercenary that can build star base and then improve defense of other star bases in area of effect (larger range).

Opt out of the bazaar and mercs, yes I think they should allow you just to turn this option off.  I always play with them on and, disabling the expansion would disable the factions as well.  I'm surprised this wasn't added yet.  Great suggestion.