I'm really more inclined to say that the hate for the male leads has more to do with certain elements of the playerbase than Bioware's writing. But you can change the writing, you can't change society.
Here are a few suggestions for Bioware
1. Players want the relationship with the male lead to matter. The problem with Kaidan was that you never really get to gain much ground with him as male Shepard. At best, you're sort of vaguely friends.
Thus, people feel like they are wasting their time. People don't like to feel like they wasted their time. With every other squad mate in ME1 you can feel their relationship with you clearly evolving.
2. People respect and admire competency. Even if you don't like the other person, you may respect them for their ability and their cause.
That is not to say at all that Kaidan is incompetent. But you are really never shown his skills and why he's useful to the team. At best, you're told that he's a decorated officer and powerful biotic. But you never see his leadership experience (No - random voice clips from Virmire don't count) and you never see his impressive biotics. Gameplay is of course not on the same level as a cutscene.
When Kaidan is revealed in the game for the first time, all he is doing is *something* in the cockpit and arguing with Joker. Joker overshadows Kaidan easily, his personality jumps off the page. You may say that this makes sense since Kaidan is supposed to be a sort of reserved character, but every good character has something that makes them stand out. In the beginning of the game, Kaidan's just some random dude, really.
When Kaidan is put into squad, he goes from random dude to random soldier. Not much of an improvement. Unlike Jenkins, you're not really given a reason to care about Kaidan. This is because you know literally nothing about Kaidan at that point. With Jenkins, on the other hand, you know about his background, his goals, and his motivations concerning the mission and why he joined the Alliance. I'm not saying that Jenkins is "better" than Kaidan, but they certainly made you care about him a lot more in the very beginning of the game.
When you meet Ashley, unlike Kaidan yet again, you get some background from her. What happened to her, her goals, and her motivations. You get a decent grip on her personality, unlike Kaidan who is still not jumping off the page.
So when DO you get a decent sense of Kaidan's background? After the Citadel quest is done and you've been made a Spectre. So that's hours into the game that he's been a squad mate and you nearly have NO idea who this person is and why you should care. Not only that, you've just jumped many ranks above Kaidan from becoming a spectre.
When Kaidan does tell you about biotic abilities, there's nothing to back them up but gameplay, which for most people is probably not very convincing. In essence the biggest problem with Kaidan's abilities are that you're told and not shown. What is he doing on the Normandy? Doing *something* to *something*.
Why on earth is this guy on the mission again? Just because Anderson says so?
If you look at the other squad mates, they all have more easily definable motivations for the mission. Everyone but Kaidan has some tie to Saren. Ashley had her squad wiped out by Saren's geth, and she wants to prove herself and prove that humanity can stand strong. Tali was hunted down by Saren and wants to prove herself to her people. Wrex has a contract to kill Saren and he wants to for once use his powerful experience as a warlord to do something good. Liara's mother was manipulated by Saren, and the whole story reveals around the protheans. Garrus investigated Saren, and wants to prove that his method of justice is what's right.
Kaidan? He just wants to do some good. That's all you learn after several hours with him. That's it.
So many people very plausibly could go through the game and feel like they're carrying Kaidan.
a. He has nothing to do with the plot.
b. You're not really given a reason to care about him.
c. You don't know what he's really adding to the team. Sure, there's Virmire - but you get to leave him behind shortly afterward. The leadership skill he shows there doesn't have time to sink in. And he's inviting you to abandon him.
On the Normandy you don't know what the heck he's doing.
d. His biotic, leadership, and tech skills are told, but not shown.
A lot of these things apply to Jacob, and in some ways, Carth. The long and short of it is that you feel like you're wasting your time with someone you don't really care about.
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Look at the most popular male squad mates for male players. Wrex & Garrus.
1. You can be "bros" with them.
2. Your relationship with them matters. If you do Wrex's personal quest he will automatically back down on Virmire. If you persuade him to back down you can tell that he greatly respects Shepard. Going from grumpy lizard to considering Shepard an old friend is a big deal.
With Garrus you can act as a mentor to him. It doesn't result in much different in ME2, but at the time in ME1 it felt like what you said actually mattered.
3. Their skills are shown and not just told to you. When you meet Wrex (with a massive battle scar on his face) he's either intimidating C-sec officers or Fist's thugs. He isn't scared of them one iota. If you bring Wrex with you to Fist he'll just brutally shoot him down. On Virmire Wrex directly challenges you. It's easy to be convinced that Wrex is a "badass."
When you meet Garrus he can tell he really wants to take Saren down. "Stall them!"
When you meet Garrus again, he manages to shoot and kill the thug holding Michel hostage without her getting a scratch. Already then, you can call Garrus "sharpshooter renegade cop." After the same amount of time you've known Kaidan, Kaidan's just uh...someone?
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All that said, Kaidan (of ME1) is one of my favorite characters. But I won't lie, there's definitely room for improvement. The lead males don't have to be the favorites of almost only female players who romance them if Bioware does things right.