Your completely right. I liked 01-03 because of the general randomness in the plot. Element-wielding robots that wear magical masks seeking to defeat a spirit of darkness in order save a tropical island. If you try to analyze it, it makes no sense, but if you simply follow the plot, it does.
For me, 04 and onwards is a love-hate relationship. I for one never really cared about why exactly the Matoran were on the island, but I did want to know about the secrets of the Turaga (they knew way too much). Also, by 03, I was really getting tired of one mystery after another was beginning to show up.