I think I have to disagree when it comes to his realism. In the world of the series a person like Shinichi or Conan can exist. And he does have flaws and I don't think Aoyama created them by accident (at least most of those).
His skills in logical thinking and his ability to pick up and learn all sorts of information is remarkable and obviously helps to portray him as the brilliant detective he is, but outside of his work he is pretty much a smartass. He thinks he is the person in charge of explaining everything, whether it's an Agasa quiz or some random thing, he also tends to do this in a very bored way which is a contradiction to its very message: Listen, listen, I know this but I will pretend like I don't really care, I'll explain it still though. This is especially predictable when he's around the Detective Boys - as soon as a case comes up he takes up the leadership, and one might argue that he teaches his friends by showing them his deductions but in reality he only shows them the end result when he puts on his typical this-is-how-you-did-it-show to get everybody's recognition. He doesn't share to many details along the line, so no one can really get an idea of his thought process, to him there's no real interest in letting people take part in the journey. He's also very easy in dismissing other people's theories, calling them idiots while pointing out the problems. Of course he tries to balance this, and gives reassurance and praise for good ideas but the very fact that he thinks of himself high enough to be in the position to laud speaks for itself.
Another issue I take is his inconsistency, on the one hand he is worrying about everyone and doesn't want them to be in danger, also doesn't really share his true feelings. On the other hand he follows his over-confident plans that can risk other people's lifes. Remember the time when he drives up to the cabin with Agasa? Or the whole Vermount-harbour thing?
I think, overall, Conan is a more likable character than Shinichi. Shinichi is a nice guy, and while he is arrogant when it comes to knowledge and his detective work, I don't consider him to be a mean person, the contrary if anything. But he seems free of flaws: good-looking, good at sports, good at what he does, popular with his preferred sex, no money-problems. So it's not that hard to dislike him, especially since his brilliance is best shown in a field of absolute misery, the detective takes a challenge to solve a riddle, and that riddle only is the objective, in the end the detective gets all the glory for the (granted - hard) work. But behind this glory is so often a dead body, a person who's life was ended, and also another who made a terrible decision. Shinichi, a lot like his great idol Sherlock Holmes, gets into an arrogant state when showing his final deductions, even uses theatrical expressions, is very far a way from a scientist but more the judge and teacher in one. So, Gosho Aoyamas genius lies in the most important plot device: what can you take away from such a person? That final moment, that is. As Conan he doesn't get to show how smart he is. No, he has to hide behind a guy who's not nearly as good as him. This basically took away his self-definition as the great high-school detective, which in turn makes Conan so much more enjoyable because he's reduced to solving cases without the glory in the end, only to have beat the challenge, to have preserved his (very black-and-white-rarely-grayish) view of justice.
The worst thing though is that he lets Ran suffer. She's waiting and waiting for a person that rarely calls, shows up every once in a while for a couple of minutes and leaves again. His love is obvious, obvious also because of how selfish he is, he keeps her around although he doesn't know when or whether he can get back to his old body. In the world of the series I look at him as a progressive person, I don't think Gosho Aoyama writes him as a possessive person but he obviously is, and while he notices it a little bit he's to comforted by being in her heart. Helping her move on seems to confronting for the person who sees dead corpses on a regular basis.
On the series:
There are bunch of things about the series itself that I grew to dislike. At first I should say that I really like it, I've been watching this when I was much younger and just picked it up again a little while ago. I think it's a very nice portrait of a modern day detective story with all sorts of different influences, the mixture is enjoyable. I also like Aoyama and his style. So this comes from a place of absolute fandom:
The world of the series is very contradicting. I don't mean the pill that shrinks people, that's actually a fine creation. I mean stuff like Kaito Kid's (who I love) masks, the way he and others are able to disguise themselves so even their loved ones don't notice the difference. This would be fine if absolute realism would not be an important part of the series: the cases most often have pretty realistic boundaries, clues and problems to them. They are most often explained by actual logical principles. So this is pretty paradox, especially when police offers pull on faces to determine if they are real - so you use a real measurement for evidence for a completely fake thing that's often a very important plot device? I don't know about that. Speaking of imitations, the whole lookalike-characters I really don't get. Why can certain characters - without much of a disguise (no masks!) - pretend to be others and no one really notices? Weird.
Why are there most often three suspects?
Also, come on, no homosexuals ever?
How come the young male characters all have a sassy, smart and athletic childhood female friend they are in love with?
Why is there this real divide between "smart" people and everyone else? You see this with Conan, Hattori, Haibara and Kid (and some others). They are all intelligent in the same kind of way. While Conan outsmarts them all most of the time, they all seem to be good at deductions, too, they instantly grasp what is behind the thinking. This is a pretty simplistic way of looking at intelligence. And I would wish this would work differently in the series' world. Conan should do a lot more research, he should ask for specific information or even do experiments. Here he parts with Holmes, who actually was often wrong, his charme was his confidence and getting to the right answer eventually.
I'm also not sure what Aoyamas view on gender-issues is. On the one hand he has all sorts of strong female characters but on the other hand they all have to be the same kind of strong, either really intelligent or karate-masters like Ran. To me the best portait of a female character on the whole series has to be Sonoko. She does not try to please everybody, she isn't waiting around like she has no own desires, she's not a pro-fighter and also not trying to score with intelligence. In a way she's the most grounded of all of them. Everyone else is in a very strange place of approval-fishing, waiting, agony and on the search for some kind of reassurance.
And, the list is much longer but this is like the most important thing: Death seems to follow Conan around and noone seems to notice? Before that child was freeloading at the agency were Kogoro and Ran involved in so many sudden murders? And whose parents would let their child play with someone like Conan? Whenever he's around some person's dead. I mean, you can't even have fucking dinner before the next thing happens. This should be handled differently.
Anyways, sorry for wrong expressions, grammatical errors and punctuation. This is not my native language.