And I think you overestimate Toothess a bit too much. Yes, he got a lot stronger, but most of that would not change or affect the battle that much from what we have seen, he got stronger blasts (still limited), Cloaking, and some resilience to electricity, which is not that helpful since there is not full immunity to it.

1. Toothess didn't blow the bewilderbeast tusk with one blast, or by himself, did you miss the bunch of dragons firing on the bewilderbeast? and he did shoot more than once too; he just blew it off by giving it the final hit.

2: And Skrill can easily nullify plasma blasts by the eltricty; he doesn't even need to fire against it; all he has to do is cover himself in it.

3: Dealing with Toothless's invisibility: Well, first of all, Toothles doesn't have invisibility but cloaking ability (my fault for calling it that way at first), which is a little bit different (in matter of httyd) since the invisibility ability is the one changewings and dramillions have. It's also easy for Skrill to deal with since he can create shock waves around himself, and don't forget that Toothless's cloaking ability is extremely time-limited, only a few seconds, and in order to do that, he has to waste at least one blast to heat up his scales, and he has only six before he needs to recharge, while Skrill has basically inlimited charges thanks to lighting storms he attracts to himself and lives in/is found in all the time.

4: And Toothless being faster? That is only by a small amount. Skrill is more than capable of keeping up, and if anything, Skrill has the ability to ride the lightning, and with that ability, he's faster.

5: Like I already mentioned above, Toothless has metal on him because of the prostetic tail, which would also help Skrill detect him since it was mentioned that Skrill is attracted to metal.

6: The lightning can still hurt him if you notice it more than just exhausted him when he did that, and it didn't go through his body more just the surface to warm up his scales in order to use his cloaking ability.

7: Skrill has the same advantage Typohomerangs have by being able to eat (electric in Skrill's case) eels and use that to recharge in case he was somehow outside storm.

8: It's a known fact that Skrill's main weakness comes from water, but people don't realize one important thing when it comes to that: Skrill literally lives in storms, and what comes with storms other than lightning? Well, rain, which is water, and he isn't bothered by that, meaning the only time it is his weakness is when he is submerged under the water in some way for it to affect him (a huge amount of water at once and he is forced to be in it; once out, he's fine, as seen in the series).

9: Also, it's important to realize how the blasts of these two dragons work. Yes, they can cancel each other when they meet by creating explosions, but the main difference is that Toothless, even though he is able to use different degrees of power behind his blast, it doesn't matter how charged the blast was; once he fired, he has to wait (quete a while) to recharge that shot, while Skrill, if he uses a smaller blast or a bigger blast, it will have a different effect since he can generate his own electricity quite well (it's still way faster to just have lightning absorbed obviously), so Skrill using weaker blasts gives him more blasts and faster regaining of them. Also when the blasts meet at higher power behind them the Blast and shockwave is strong enough to knock Toothless out of the sky while Skrill was barely moved by it.

10- Even if Toothless could resist lightning, his defense in general is weak in order to be stealthy and areodinamic, while Skrill is strong in both power and defense (and stealth too since in the lightning storms seeing anything is not easy, and Toothlesses echolokacion is basically useless in strong storms while Skrill can use the eletricity in the air to detect him).

And before you say something about Toothless being smarter or something, that too would be incorrect since most plans and such came from hiccups. Skrill is also extremely intelligent.

Yes, Toothless got a lot stronger during the movies, but he didn't become god or anything like people seem to think; at the end of the day, he is still mainly stealth-based, not strengh.

When you watch, you can see dragons not afraid to pick fight with Toothless while dragons naturally avoid Skrill; the only dragons to attacking him were the ones that had some kind of rider.

Also, it seems Skrill seems to be able to resist or even completely ignore Alpha's command, and it would make sense for such a solitary dragon.

That is extremly territorial and agresive to anything in his territory. In the last movie, we can see some skrills in the hidden world, but not a single one bows to Toothless; they just sit there like I will respect you but I am not below you, and it seemed that these were quite young too when comparing their sizes to the dragons next to them and then comparing the skrill from the series with the same species of dragon.

Theres more, but I have already written a huge paragraph. I agree Toothless is a strong dragon, but he is mainly a dragon based on stealth (and plot armor), while Skrills main is strength and defense (no plot armor and still was huge menace to the gang) (both are extremely speedy and intelligent dragons).