... MMBN4 was the worst by far.
The story mode was crap. The story itself was very meh, and then the fact that you would have to play through it three times just to essentially "beat" the game was also pretty bad. In terms of battling I remember it being worse... but I admit I haven't spent enough time with it to say that the battling aspect was "worse" than MMBN5.
Speaking of MMBN5, liberations are cool! A bit tedious at times, but cool imo.
MMBN6 was the second best one of the series, and because of how late it was if there were to ever be any competitive scene for MMBN it would be on that OR the DS version of MMBN5(if only for wifi capabilities; I ain't traveling for this game).
MMBN3 is the best in terms of playing through the game as well as the amount of variety found against the bosses in the game. Otherwise the battle system was "cheap" because of the allowing of multiple versions of a program advance and, honestly, the custom glitch.