While not perfect, Hato is a far more nuanced take on this subject than Megumu. Actually, Genshiken Nidaime's flaws may add more to the series than it takes away. I haven't actually seen the original Genshiken, so anything I say from here on out is about Nidaime, alone.
For those who don't know, Genshiken is a series made by otaku, about otaku, for otaku. The titular "Genshiken" is a university club dedicated to the otaku lifestyle. One of the members, Hato is a fudanshi (a boy who loves BL) who cross-dresses to fit in with those who share his interests. At least, that's how it starts out.
Genshiken doesn't have a single "main character." It tries to give all the club members close to equal focus. Hato is one of a few characters who gets a bit more focus than others, though. His character arc is about self-discovery and acceptance.
As I mentioned, he started cross-dressing because he felt he'd be more accepted as a girl who likes BL than a boy. He's found out almost immediately, but he keeps cross-dressing because it's more comfortable. Over time, he also realizes that he just likes cross-dressing.
This doesn't pose much of a problem, since most of the members see it as another hobby. They all have weird interests. What's wrong with cross-dressing? The one character who does complain about it does so because of her own insecurities.
One thing that makes this take so great is that it does bring up the otokonoko genre. The series is about otaku culture, so it makes sense they'd draw comparisons. What's great about it is that it goes out of its way to differentiate fiction from reality. There are jokes made, since they're all otaku, but the series treats Hato like a person, not an object.
I could do a whole review on Genshiken Nidaime and how it handles this subject, but this is my brief thoughts. Overall, this is a great, nuanced take on this subject. I enjoyed it a lot.
As for Hacka Doll #3, there's not much to say. For one thing, HDTA is very short. It's 13 episodes, and the episodes are each 7 minutes long.
On top of that, #3's one of those otokonoko characters who just sort of...exist. That's not necessarily a bad thing. Some cross-dressers do just sort of exist without any special motivation. His gender isn't even treated as a big deal, since it's only brought up in one episode.
If I wanted to, I could criticize the fanservice moments. They're not very frequent, though, and they could be seen as part of the joke. Hacka Doll is a pure parody show. It has as many references as Genshiken, and it's never trying to be serious. How much any of the content bothers you depends on how much you're willing to go along with the joke.
Hacka Doll #3 isn't a complex character, but he's good enough. He's got some funny moments, some clever ones, and even some heartwarming ones. He's alright, and I enjoyed the anime for what it was.
And now I'm free to move on! The next show I'll be watching is Namu Amida Butsu!: Rendai UTENA.