Yea it's not the same reason as to what is the best 6v6 set up. To be honest, Destro does not run Marauders in 6v6 in the best set ups. You are conflating things. Marauders are certainly destros top city dps class at the moment, but they aren't for 6v6.
To give you a little more information - the Marauder's strength comes from it's AoE spec, which like most AoE specs, gets worse and worse the lower amount of players you have. In a 6v6 setting, AoE is in general, not going to do a whole lot of anything besides break staggers, so what makes Marauders strong in city (and/or wb vs wb settings) is just not applicable in 6v6. In fact, the Marauder 6v6 specs are completely different and don't involve speccing into the AoE path (monstrosity) whatsoever.
Either way, they aren't a great 6v6 choice because you can just cover the Mara debuffs via other classes (BG has most, get a heal debuff from you other DPS), and run a DPS class who brings more to the table (as well as more ST DPS), such as a WE or a DPS DoK, which tend to be the premier dps choices for Destro 6v6. Choppa is in a similar place to the Mara more or less, and not considered very viable.