I read the MM manga a long time ago so I don't remember too many details, but I agree with your assesment of it. The Ikana section was especially poor. The manga takes arguably the one of the richest segments of the series and reduces it to a dull boss battle. The depiction of the Mask Salesman was completely messed up, with him revealed to be evil at the end, which made little sense. The backstory about Majora was interesting, but it was nothing more than fan fiction and it didn't shed too much light on things. I remember that I liked the beginning and that there were some great moments, but overall I was disappointed.
I loved the Oracles manga, on the other hand.
OoT's was okay. I really liked the part when Link was in the desert and had a vision of the Deku Tree, if my memory can be trusted.