What is illegitimate about a tournament?
One division is suddenly going to change it's ranking/championship format from the rest of the organization? That screams illegitimacy. Furthermore, it's also wildly unfair to the champ, whose already had to work his way through the division. Let alone if it's a division with a defending champ.
This format only works when there is no champ in the division. Then it becomes a natural tournament (see addition of the flyweight division).
It absolutely insures that the fighters that should be fighting, actually DO FIGHT
No it doesn't. Injuries, medical suspensions, and withdrawals are all still common in tournaments. MMA tournaments have always seen random and bizarre matchmaking for that reason. I mean FFS, look at Strikeforce's infamous HW tournament. Fedor got eliminated in round one, Overeem dropped out and jumped to the UFC, and an alternate in Cormier ended up winning the whole thing. Cormier wasn't even a well regarded HW at that time, that tournament was his coming out party.
I suppose money matches and weight-class jumping is better than having a system where the fights are exactly laid out, and the winners fight the winners?
The only reason that's happening at such frequency is because the WME is pushing it. A tournament format isn't going to magically fix shit if WME doesn't want it fixed.
Zuffa ran a ranking based UFC for years with great success. By nature of prize fighting, exceptions are going to be made, but Zuffa did a pretty great job of trying to honour the rankings in most instances.
Also, a champ couldn't take a year or more off like Conor and Bisping, etc.
Unless they're injured, that is again a matter of the organization enforcing/working a schedule. That's not going to change with tournaments.
I mean FFS. We saw PRIDE run tournaments for years, and it muddied the waters over there more than anything. Even Bellator's tournaments grew frustrating to the champions, and you'd often see them out for long stints.