About the belts: The Japanese are all about tradition, heritage and lineage. So for a belt to have a decent amount of respect, it's gotta have history. All these old belts are from other promotions and were passed on to these promotions in different ways and have a lineage and history that goes back decades.
Different case with NOAH and the "Grand Honored Champion" belts, which are all new. However, they are working on building those up with a line of respectable and generally kickass champs holding on to the belts. All except for Rat Boy Ogawa. He was a champ because he made a great cup of coffee...
Two hours later they decided to stop at a diner Because they loved the smell of eggs and coffee I just had to smoke a cigarette and wear a hat By the time that they set off again, the sun was starting to set It made the sky look red like a nuclear ray One of them said "what do you want more than anything in this whole wide world Do you want money, do you want sex, or do you want all that success?" I thought about that one myself (Then they came upon the thing)
From, "The Church of Logic, Sin and Love" by The Men
What does NOAH stand for? No nonsense wrestling, of course, har har.
Anyway, someone once told me Misawa just liked the biblical connotations, since the company was formed when he took off with half of the All Japan roster (sorta like Noah and the ark, but with wrestlers). Plus pretty much every tour has the word Navigation in its name (Navigate For Evolution, Encountering Navigation, etc.)
As for the league crossovers, they happen so often I guess they're not really a big deal. Do they get boring? It depends. The New Japan vs. Noah juniors feud was probably the best feud of 2002 in terms of matches and drama.
It's not a rebellious thing. It's out of habit. Just like people will still call WWE the WWF. It's called a habit. It's what people are used to calling it. Eventually, everyone will call it WWE... out of habit.