I really don't see how there is substantial evidence to back your claim. You presume that because Celestia has "ruled" over Equestria for a thousand years and that Equestria has apparently prospered during this time that the former is necessarily the cause of the latter. Unfortunately there is not enough evidence to support this claim because any information regarding Celestia's level of involvement and influence on the functioning of Equestria is not given enough focus so you're just talking out of your rump. Correlation does not equal causation.
https://yourlogicalfallacyis.com/false-cause
And you also state that because Celestia has ruled for as long as she has, and is apparently the only recognizable ruler that Equestria has ever had, that she inherently proves herself the most qualified candidate. This is nothing more than a circular argument. You might as well say she's the best because she's the best and it would have as much substance. If the only standard for someone's ability to rule is their age then that's just nonsensical ageism and discrimination, and experience isn't everything. There's no way you can know that somepony else wouldn't be just as qualified as Celestia is at governing because it's a undemocratic system that doesn't allow frequent changes in leadership.
https://yourlogicalfallacyis.com/begging-the-question
Dualistic diarchy it was intended to be? Wow, I'm so glad that we have you here to shed your exclusive insight on the political destiny of a fictional world. If Equestria was always meant to be a "diarchy" then why was it able to supposedly prosper so much with Luna banished to the moon? It would seem Equestria doesn't really need princess Luna around when Celestia can raise both the sun and moon. However just because I said that doesn't mean I agree she's the best possible ruler, I don't believe sheer magical prowess is an indicator or precondition for governing ability. Trixie in the episode 'Magic Duel'(S3,E5) is a prime example of this.
https://yourlogicalfallacyis.com/genetic
If Equestria was not what it was meant to be for over a thousand years and both Celestia(for banishing her sister) and Luna(for betraying her sister, causing her banishment) were responsible for this then that would clearly contradict your earlier statement that they are the ideal rulers. The fact is Luna jeopardized the security of their kingdom by virtue of her petty jealousy.
Celestia can be considered the best ruler for Equestria largely because she's been the only ruler of Equestria, not counting villains like Discord and Sombra who are clearly painted in a negative light for characterization. It's also important to consider that there is very little known about the actual details of her tenure other than that everything seems to be mostly okay most of the time except for when a crisis emerges and she gets Twilight and Co. to deal with it. How outstanding.
Since Celestia is obviously not a villain and intended to symbolize a motherly role model to be emulated it's obvious why the creators would try to give her practically zero flaws and present her as perfect. Certainly it's an easy way to avoid any actual development for her despite making her somewhat boring in the eyes of many. But the thing with perfection is that it's entirely subjective, and Celestia's character, and her position as the matriarch, qualifies as anything but perfect to me.