"Smac1, Chuck was ranked no1 before his fight with Rampage (which is when these rankings were made)."
How? Who did he beat to magically get that ranking? There is no world where Lidell ever made sense as #1 except "I think he is the best". He certainly never had the wins over the top guys to warrant it. Has he ever beat a top 5 fighter in his career?
"In no other sport does a fighter immediately replace the opponent he beat in the rankings."
You don't know much about combat sports rankings do you? See boxing, kickboxing, Muay Thai etc. for examples of sports that do their rankings in exactly that manner. The whole point of rankings is to figure out who should fight the champ next. The champ is always ranked number 1 (except for rankings that refer to the champ as "Champion" and start numbering from the top contender). In MMA because of the separate orgs this is difficult, so the number 1 guy is typically the linear champ. See Ring magazine's definitive boxing rankings for further detail on how to rank fighters in combat sports.
Couture being above Gonzaga is ridiculous. Couture has 1 heavyweight fight in the last 5 years, and got stopped in 2 of his last 3 HW fights. Gonzaga is 8-1 during the same time period with 8 stoppages and a recent dominating win over tougher competition than Couture has ever faced let alone beat. Hell Couture has lost half of his last 10 fights at any weight.
Serra is the undisputed #1 WW. He decisively beat the champ, if it turns out he does not deserve this the rankings will self correct the next time he fights. As of right now he earned it by any measure other than "I don't think he is the best" which has nothing to do with rankings.
Arona has lost 3 of his last 4, and has 1 win in the last 6 years over top 10 LHW competition. you apparently anointed him number 4 based on 1 meaningful win (and he lost the more important rematch).
"Sokoudjou has two wins over top 10 fighters and got into the top 10."
He has back to back destructive KO wins over top 5 competition. There is no objective or subjective system in the world that has him out of the top 5 other than "I like these other guys better". He has more wins over top 5 competition this year than Arona or Lidell have in the last 5 years.
"If Billy McIveneverheardofyou, ranked 254th in the world, from some swamp in Louisiana beat Tiger Woods in a golf match would he immediately be ranked no 1?"
If he followed it up by beating Phil Mickelson so badly that they didn't appear to belong on the same course, and 2 or 3 rounds of golf a year was all that golfers played... yes he would. Golfers play hundreds of rounds a year. This is a ludicrous analogy.
Honestly, it seems like you ranked the fighters based on who you think is the best instead of any sort of reasonable approach.
"I don't expect everyone to agree with all the rankings as they're always fairly subjective."
When 2 guys have not fought you might have a subjective decision to make between who is 2nd and who is 3rd. Otherwise rankings done right are quite objective.
For instance there was some debate over who was 2nd and who was 3rd at HW (since Nog beat Cro Cop, Cro Cop beat Barnett, and Barnett beat Nog). This debate continues because Gonzaga's win over Cro Cop puts him in either 2nd or 3rd depending on how you subjectively determined who was #2 and who was #3. Personally I think Nog's avenging his loss to Barnett cemented his #2 ranking, but others will argue (validly) that Cro Cop destroyed Barnett repeatedly while Nog went to two decisions, 1 he clearly lost, and 1 he won a close decision.
How the hell is Kosh right behind Diego who he just clearly beat?
How is Sherk who has NO wins over top 20 LW's EVER magically number 5? He has done nothing whatsoever to justify being in the top 10. He has no wins over top 10 competition in his entire career at any weight class. It seems that you are using the back in time machine ranking system to move Sherk up the rankings. His win over Diaz at a different WC when Diaz was not top 10, does not move Sherk up the rankings now because Diaz beat Gomi. This is the same back in time machine ranking people used as an excuse to move Lidell up the rankings when he beat Babalu who had a win over a young and inexperienced Shogun.
As ridiculous as we might think the decision is Diaz has no official wins at LW and can't be ranked. If he was he would be the undisputed number 1. Sakurai is the only other logical choice, who BTW has a win over your #1 in the last 2 years, as well as a win over Hansen... who Aoki beat to magically become #1 in your rankings. So Aoki loses to Sakurai and beats Hansen to magically become #1, but Sakurai beats both Aoki and Hansen and is #7. That's beyond subjective, that's fanboy.
Aoki is probably the best LW, but he has NO WINS over top 5 fighters EVER. He is clearly not #1.
Your notes contradict themselves at almost every turn.