Personally, I think that characters made for one specific purpose or according to one specific trope are not likeable, while characters who have something to go for them tend to be likeable even if I can't relate to them. When you said you're good in making dislikeable characters like a jerk or villain, I immediately wondered whether you actually make good characters or annoyingly bad ones. Does your jerk have some other sides to them, or do they seem to be just a jerk for the sake of the plot? Is a bully just a bully to make the protagonist seem like a likeable underdog, or does he have some relatable traits? Is the villain some B-list 'I'm evil because I'm evil!' or does he have an ideology that clashes with the hero or the world resulting in his villainry?
I think the best way to illustrate my point is with a few examples:
From all the tropes, you have characters that excel to greatness and characters that are just cardboard cutouts with no character depth. I'd like to focus on one of the most polarised tropes of all: the yandere trope. They can be separated in:
1) A yandere for the sake of a yandere. These girls just seem to love the MC and kill anyone once the plot demands such a situation. In the most stereotypical and short yandere stories, the yandere doesn't seem to have any other sides to her than the girl who's interested in you for unknown reasons and the murderous sociopath. These can be fun for some when the game is campy enough, but they're not exactly memorable or good.
2) A yandere who actually has any character depth aside from the above. Once a story starts to see a yandere as an actual person in the story, they can add other character traits to them. What is she like besides in love? Why did she start to obsess over the MC so intensely? What are her hopes and dreams aside from the MC? Even the most Yandere of Yandere have some other character traits to them aside from their trope if they're any good.
Jojo's bizarre adventure. I loved the Phantom blood series but hated Stardust crusaders. Why? Because of the villains. The Phantom blood series featured several likeable or at least not-2D characters. Dio had a very defined character, the pillarmen cared for eachother's wellbeing and respected their opponents, and even small-time characters like the Knights of Bloody Mary were respected by the story (although that story is kind of askew). This series respected their villains. Stardust crusaders on the other hand featured almost exclusively despicable villains that were meant to please the viewer by getting the sh*t stomped out of them at the end of the episode. These villains could be catagorised as either a gravely misformed human who remained hidden until the heroes beat him so they could laugh at his appearance, or a good-looking but very arrogant and cowardly villain. None of these were likeable or memorable.
While the two series above give a better example, comparing the 90' Jojo series to the modern one would also be a good way to look at things. The 90' series scrapped pretty much all the unlikeable villains, leaving only the ones with some redeeming characteristics like the blind man or the poker player. And their Dio remained a respectable one, unlike the new one who suddenly grew green lipstick at the end(?).
The bottomline of these examples: likeable characters have more to them than just what the plot needs of them.
If you don't understand what I'm saying (I can write things rather vaguely at times), feel free to ask further or give me some series that you are familiar with to make examples out of.
*Edit:
1 - Don't show Author Favoritism towards the character.
Also this. Very much this. I briefly touched upon this topic with Mary Sue-ism, but one cannot say this clearly enough. Never favour one over the rest too much.
3 - At the beginning of the visual novel, show a scene where the character is doing something nice.
True, a good trick that is used in a lot of stories. Make sure it doesn't seem too forced or detached though, whether it's an action scene for the sake of establishing someone as a badass, a tragic scene to justify someone's angst, or a villain scene to show the nefarious depths to which the villain can stoop, never make it feel like the scene exists only for that purpose. And don't overuse it, if every character gets a scene like that, it will quickly become annoying.
6 - Don't make the character a coward or a traitor.
I'll have to veto this one though. If it works, it works. I liked Joseph Jostar character
because he could be a coward at times, who remained rational and kept running away or using an underhanded trick as viable options if deemed neccesary. You should off course never make someone purely a coward or traitor, even if that's the only purpose of their character to the plot.