You really going to cite Regigias as a 90-10 matchup? Really? They one hit your main attacker, are capable of continuous power lock, are capable of out-speeding you are you list it as 90-10?
I call shenanigans.
First of all, a 90-10 matchup does not exist in this metagame. Just about any deck is capable of a bad start/donk and techs can easily account for 5-10% in any given matchup. Matchups should realisitcally be 25-75/30-70 at their lowest.
Secondly. PERSONAL EXPERIENCE MEANS NOTHING, especially when you supplement everything that didn't go your way with incorrect Theoreymon.
However, since this is mindless bashing, ill give my input on each of your "Matchups" as well as one you forgot.
Dialga G + Variants: Deafen is difficult in this matchup, and you must choose how to set-up carefully. Get a Claydol out Asap and work on setting up a benched Hippowdon. Make sure if you bring it active that you can kill their Dialga G Lv.X in the same turn, because Hippowdon Lv.X has a hefty retreat cost without rainbow float. Watch for Power spray on Sand reset, try to bait them into an unfavorable position beforehand. A good Dialga G player will Opt not to use uneeded stadiums here, so you probably won't get much use out of Flygon's first attack. Still, once you get a Flygon Lv.X powered up you should be able to pull it out, by sniping any level X's they have, still, they tend to outspeed you so play it carefully.
Ruling: Flygon 60 - Dialga G 40
Dialga G/Palkia G: You max out at 80 damage in this matchup due to Palkia G's power. In addition, be careful of weakness on Hippowdon. Like the dialga G Matchup, you still need to watch for power spray, but you also have the added problem of Mesprit locks to deal with. If they manage to prevent Trapinch from getting his power off then you are in trouble. Build a Flygon X on the bench and snipe what you can before they revenge kill you. It's a difficult matchup, but through usage of Flygon Lv.X, you should be trading 2 prizes for every one. Still, This is more difficult then straight Dialga due to weakness and their ability to power lock/snipe you bench.
Flygon 50 - Dialga G/Palkia G 50
Legos: Similar to the Dialga/Palkia matchup, this depends on the number of Mesprit's being run by your opponent and how quickly they can snipe your bench. If they can slow you down enough through power lock and hit your benched Trapinch/Vibrava's then you are in trouble. Strategy is very similar to the last. Don't worry about Hippowdon and go for broke in getting a Flygon Lv.X set-up. If you can snipe the Palkia X then you have a decent shot of winning, but only if you can do it while a reasonable amount behind. A difficult matchup
Ruling: Flygon 45 - Legos 55
Kingdra: While it has seen a considerable drop in play, it is still a viable deck. However, you have one major ace in the hole against Kingdra. Vibrava. Vibrava renders Aqua stream useless against Flygon. If they Aqua stream with less then 7 energy in their discard then it is weaker then a boosted Dragon pump, but if they don't then you can hit their active Kingdra for 140+ with a Vibrava and change the tide of the game. They do have a speed and weakness advantage though, as well as the ability to donk early, so it's still not a positive matchup, just remember exactly how good Vibrava can be here for turning the tide.
Ruling: Flygon 45 - Kingdra 55
Ttar: You don't use very many powers outside of Trapinch, and you can Utilize both Sand reset and Tyranitar's weakness extremely effectively. This is probably one of your easier matchups, just watch out for a Sableye donk or a quickly set-up tyrannitar. Still, barring bad starts and prizes, you should win this more often then not.
Ruling: Flygon 75 - Ttar 25
AMU/PAMU: Battle of One hit Ko's. They one hit you with Supreme blast and you One hit them with Both Flygon's second attack, and Xtreme attack, although if snowpoint is in play, only the latter is a One hit KO. This is not an issue because of Flygon's first attack however. Allowing you to do 40, discard the stadium, and follow up with a Ko the next turn. The speed difference is noticible, but not substantial enough to cause major problems, Flygon has the edge here due to Flygon Lv.X, but watch out for supreme Blasts.
Ruling: Flygon 60 - AMU/PAMU 40
Toolbox/Toxitank: They can outspeed you and donk you, but if you manage to get a Flygon powered up then you should be able to win due to the invincibility provided by the first attack. The only major threat toxitank poses is the donk, which should still be watched for.
Ruling: Flygon 75 - Toolbox/Toxitank 25
Gengar + Variants: A difficult matchup. Gastly Trainer locks you preventing you from getting an early Flygon. To make matters worse, Trapinch has a power, meaning it can actually be donked by shadow room(LOL). They have resistence as well, meaning you won't get any OHKO's against them. In addition the coin-flip further throws the matchup in their favor. Although you can Circumvent the Coinflip through careful Usage of Flygon Sw, this is still an incredibly difficult matchup due to Shadow room sniping benched Trapniches and Coin flips taking care of your active Flygon. Anti-gengar techs(De-evoluter) are highly reccomended.
Ruling: Flygon 35 - Gengar 65
GeChamp: This matchups difficulty lies solely in who they start with. If they start with a Gastly, then it's as tough as Gengar, if they start with Machop then the fear of a Shadow room donk is gone, as well as any immediate threat to the active flygon. It takes 4 heads on hurricane punch to knock out a Flygon, however you won't get much usage out of Flygon X in this matchup outside of the extra HP and mill. X-treme attack does do 190 damage to machamp level X, but you should rarely have to use it like that. Hippowdon is dead weight in this matchup due to low energy costs for Machamp and Gengar. Still, it's a little easier then Gengar
Ruling: Flygon 45 - GeChamp 55
Machamp + Variants: Much easier then Gengar. You have an advantage here due to Take out only doing 40 damage and you being able to hit for much more damage much faster against them. Hippowdon is pretty useless, but their main attack against you is luck-based, while yours is most certainly not.
Ruling: Flygon 65 - Machamp + Variants 35(Matchup changes to 40-60 if Machamp player is using Rigged dice)
Blaziken + Variants: Finally a simple matchup. They rely on Heatran for consistency and you can snipe Heatran easily. In addition free retreat makes it simple to get Away from burn, and Hippowdon can mess them up once they get set-up. You have an edge in most places here, and the matchup reflects it accordingly.
Ruling: Flygon 70 - Blaziken + Variants 30
Speedrill: Beedrill can one hit you with one energy. In addition, it doesn't have to play a stadium if you drop your own time space tear. It is for this reason that it is reccomended that you do not drop your own stadium. If you can force them to use a stadium then you can 2 hit a Beedrill safely. Still, Beedrill one hitting you is a Problem. Level up quickly and hope that they don't have enough pluspowers/bucks to one hit your Level X. Hippowdon is pretty useless here thanks to the cheap attack cost of Beedrill
Ruling: Flygon 40 - Speedrill 60
Regigigas: The Most important part of this matchup. Regigigas can One hit your main attacker as well as your level X. Being as you cannot evolve and level up in the same turn, it is Highly reccomended that you wall with Hippowdon while setting up a flygon on the bench. Once the Hippowdon dies, bring up the Flygon, level it up, and Kill regigigas. This sets Gigas back pretty far, but If Gigas runs Mesprit then they will without a doubt outspeed you. This matchup depends on how far you get behind and when you use your Sand reset Poke-power. No matchup where they One hit-Ko your main attacker is easy, and this is no exception.
Ruling: Flygon 50 - Regigigas 50
Holy Handgrenades, an accurate matchup!
Torterrible/Shaymin Variants: The reliance on Shaymin is too heavy and easily KOd with Flygon. Torterra is a force on its own, but can be taken down with Flygon RR and a good bench on your part. If they are foolish enough to play a dawn's, then grab the opportunity and protect ftw.
Ruling: Flygon 65 - Torterra 35
Flygon + Mirror: This is the most interesting test I have done as the weakness to colorless on the RR Flygon lineup means its back and forth KO. Use the advantage of strong supporters and drawing power to setup faster. It is the only way (obviously strategy must compliment this) to win a mirror when the mirror is so potent.
Ruling: Flygon 50 - Mirror 50
Porygon- They outspeed you and only need 2 energy to attack. They also don't need to drop the level X, meaning you are trading prizes at a Poor ratio with them. Sand Reset is Key here. Use it when they have 4 or more Tm's on the field and it will set them back quite a bit. Still, even with Hippowdon hitting their Weakness, they outspeed the Hippo and he can't respond with One Hit KO's. Definetly in Porygon's Favor.
Ruling: Flygon 35 - Porygon 65
There, there are some more believable matchups for you. Now, the predictable response will be "I tested over 90 games and you think I don't know my Matchups?" My answer, yes. Not accurately anyways. I'm going to borrow a comparison from the Video game world here.
In Video games such as Smash brothers(Melee, Brawl) Tier lists are determined by two players playing at an equal skill level. This is the first problem with your matchups. We are to inheritely believe that your opponents are as good as you. I for one cannot believe that when reviewing your matchups.
Secondly, your metagame- You claim that you have faced 16 different competitive decks numerous times. Georiga Regionals, with your established metagame, had a grand total of 6-8 different decks in T16. Either everyone around you plays pokemon, or you have friends building decks with the sole purpose of testing against your Flygon. This is a form of Bias not commonly recognized.
By having someone else build a deck just to test against it you are losing some crucial factors. There is the abscence of techs, the occurence of Misplays, and the Inability to have tweaked the deck to their liking. In your case, having Proxied and played Flygon for quite a while from what i gathered, you have had the opprotunity to eliminate misplays, find suitable techs, and tweak your deck to how you had seen fit. That automatically sways most matchups about 15% in your favor.
I'm not personally attacking you, I'm simply saying that you can claim your not Biased, but unless you compete against all these decks at a Premier event level then your matchups are no better then theoreymon. From a certain perspective, they can actually be worse.
Also, run 4 call energy, it's the best card in the format.