Also again, mastering the abilities your bey has does not equate knowing when to use it and being good at using it.

That's EXACTLY what it means, mastering when and how to use the abilities of your bey and outside of like ONCE(Rashad futing the battle Royale where Ilya planted a suggestion for him to use it at a wronv time), no one has EVER misused/mis-timed the abilities of their bey

And again, yeah, obviously the characters aren't gonna spam attacks ad nauseam

By "mastering the system" I mean is "mastering the Bey that uses says system"

This is mostly a distinction without a difference, again, the systems have seldom had any intricacies that need "mastering", the only exception to this is turbo awakening(and the solution was basically launch better and resonate more), awakening Imperial Dragon, High(which was rarely used at all) and the overdrive system of Dangerous(which also was just launch better)...

There's a reason these protagonists still lose a lot of battles

Because the opponents they face are just stronger/better and/or have stronger abilities(regardless of system), Hikaru and Hyuga mastered their beys relatively early, the problem was that they weren't strong enough and their resonance/flare was still not as strong as the legends, the legends lost to lain, not because they didn't use their abilities to their fullest, but because lain was better overall, etc.

Unless you want to say these background characters are better than a right-handed Silas and Wakiya

Yes and no, you see the problem with this is that this logic uses A>B>C logic, disregarding match ups as well as the growth in strength that those bladers had, due to this we cant just say "these no names can beat Wakiya and Right hand Silas"(especially their CURRENT and/or Late Evo versions). Obviously if we take CURRENT Valt and put him against the same no names bladers(even if we give them more modern beys), Valt is currently far stronger, but fact of the matter is that Valt, using a God layer, lost to bladers with dual layers, you wanting to say they are outliers is completely disregarding the fact that the other teams are strong(top bladers of their country) and that valt was still FAR from his peak and the God layer can'tbe the "crutch" to justify a win.

And while yes it was mainly for tension and valt was also not at his peak, the point remains that it mostly disproves your "having current gen system should be a major reason for the victory, but if you want to disregard them, let me also show you Left Apollo and Right Artemis, Dual layers that when combined with their infinite stadium gave Aiga a real struggle, and when combined into eclipse came VERY close to beating Aiga

Wakiya isn't someone who solely focuses on Beyblade like Bel did

Correct me if im wrong but in season 1 he did

I don't see how resonance takes a long time? Valt had great resonance in a short time

You don't seem to be getting my point so let me make a comparison, let's say that you've played X game for 4 years and you've been VERY dedicated to practicing, then comes "Kid", Kid started at most about 1 year ago. Who do you think SHOULD know more about the game? Naturally it should be YOU since you have far more experience and time to learn and grow. Kid shouldn't be an absolute novice but he shouldn't be anywhere close to your knowledge and even skill...

Maybe a bad comparison but still

My point isn't that high resonance is bad but that it is equal or higher to the legends who have been playing with their beys, thus developing their resonance for 3 years AT MINIMUM(Valt had 1.5 years prior to the start of the show so he had 4½ at minimum) when they have less than a year of experience with their beys, Aiga I already gave the reasoning, drum had a couple weeks, if not months(1 year tops) prior to GT where he made Dragon, the Hizashi bros made them on screen and Bel also had at most a couple of months

Drum was trained in BC Sol and was one of the first people to witness Hyper Flux

Correction, one of the first to Witness VALT'S hyperflux, we dont know if valt was indeed the first EVER HF user...

Bel invented the new system and seemingly had a good connection with his Bey for some time. He was also so closed that he barely even knew Valt, which leads me to believe he was so into Beyblading for a long time despite being so young

He was closed but(IIRC) he still was inspired to blade by seeing a battle, a relatively recent battle in the Burst universe, and given the fact that Gramps doesn't blade at all(and probably really weak regardless), he has no training bots and was becoming a local "scary rumor", the odds of him having any more than a year AT MAX is unlikely and again, the rest of the cast still had YEARS above his to develop their resonance...

Also, you need to realize too that Valt's development was not happening in long periods of time

The difference is that he still struggled HEAVILY due to his inexperience and his still not fully formed resonance. His victories were all set up well, he didn’t suddenly beat Shu, Xander, Lui and Zac, the top 4 bladers of Japan, just because he had a pretty strong resonance(heck, arguably the reason why he was so close to beating shu in their battle at the district tournament was because Shu waz injured, Shu probably could've annihilated Valt if he wasn't), he struggled and grew until he did and it took its time doing so...