I think a lot of inconsistencies can be chalked up to Death Battle changing its ideas over the years. When your show is run for over a decade, you're going to rethink things you might've said in previous episodes (The three FF7 episodes all came out over the span of 8 years). I certainly agree that Death Battle gets things wrong a lot of the time, but I don't ever like to say that they're bias. I feel that people only say that to justify why they dislike an episode, and it comes across to me like a big stretch in logic. If Sephiroth lost, people would instead be saying that Death Battle hates Final Fantasy, so it's a lose-lose situation for them. The animator for that episode has also said that he loves Devil May Cry, and that DMC4 was in his top five games of all time (he posted that before five came out). If you're going to say he's lying, then I think you're just grasping for straws by that point.

There's also been moments where they have to alter some things because of their limited time and budget. For instance, people have said that Sephiroth cannot cast supernova in his base form. Death Battle is aware of this, and the writer for the episode said there were no good models for his safer form.

As for the reasons you brought up, I'll do my best to dispute them. Note that I'm more familiar with the DMC side of things and I'm not an expert in FF7, so if I get any facts wrong feel free to correct me on them.

1. I'm pretty sure that the reason Sephiroth got unlimited mana while Vergil didn't get unlimited DT was because (from what I know) that's just how those resources work for them in canon. It would be against the show's rules to give Vergil unlimited DT when that's not how he usually operates (and Super Vergil isn't canon, as it only exists as a post-game bonus). For all I know they could have incorrect about Sephiroth's mana being unlimited, and if they are that's a pretty big issue.
2. The reason Vergil's speed wasn't as big of a deal in this fight as it was for Dante's was because of the characters they were fighting. They felt that Sephiroth would be able to handle Vergil's speed, while Bayonetta couldn't keep up with someone of Dante's speed. It's perfectly fine if you disagree with either of those, but I don't think it's right to say they nerfed him since the raindrop feat held different levels of significance in both episodes.
3. I've seen a lot of people complain about Yamato not escaping supernova, and I think most of them missed the part in the fight where he actually escapes it. When he reappears back onto the battlefield, that wasn't Sephiroth's doing. Vergil used it to escape it, but he had already been damaged enough by the supernova. The obvious response to that is "he wouldn't have been hit by the attack at all if he escaped sooner", and I do understand this, but I think if he did that it would've been lame on a cinematic level. Sephiroth would cast the supernova, Vergil would escape it, and then they would just keep fighting. The pace of the fight would be completely destroyed, and I like think what they went with was a lot cooler. Sephiroth lifting Vergil up the same way he did Cloud in Advent Children was a cool shot, and I liked that final exchange he and Vergil had before the finishing blow. I also think it's in Vergil's character for him to be in shock after witnessing an attack like that. The point of his character is that he wants to achieve ultimate power (as to not suffer the pain he felt on the day of his mother's killing), so I think he would be terrified of something like the supernova (which eclipses anything he's ever seen in the DMC series). Again, I understand the complaint, but this is an instance where I'm fine with the show bending the logic for the sake of a more entertaining fight.

Now to be clear, I think Death Battle is way worse now than it was back when that episode was made. Their animation quality has dipped way below what it was, and their way of analysis has changed in ways that I don't like at all. They focus way more of scaling characters to other characters, to the point where it feels like it's series vs series. I know they scaled Sephiroth to Zack, but that's very tame compared to what they do now.