What I think makes a good shoujo is the main character(s). In the case of a main female character, she needs to have a strong will, not a dumb a** crybaby, can stick up for herself, and doesn't feel like she HAS to be in love and have a boyfriend. I also really don't like the girl who can't decide which guy she likes. Other than that I'd like the girl. In the case of the male main character, he can't be an overly possessive / abusive guy who thinks it's alright to punish / "rape" a girl if she does something he doesn't like. These kinds of guys care more about themselves than their love interest. A good main male character would love only his love interest and not play around with other girls, and respects his love interest.
A good shoujo manga doesn't need to have great art to be a good story, but it doesn't mean that I don't get bothered by it sometimes. If the art is so bad, It might take away from the story. And vice versa, really really good art can enhance a good story, or make a horrible story seem better than it really is.
Some examples of shoujo manga with bad / mediocre art but have a great story...
Tokyo Crazy Paradise ,
Sora wa Akai Kawa no Hotori (Red River), and
Kanata Kara (although the main character from Kanata Kara was a little too weak and crybaby-ish, the overall plot helped make it one of my favorites.)
And all that ties in with a good plot, even it the characters have good personality and good art, if the story doesn't have a good plot, it won't last long, and if does last long, it'll just feel dragged and boring. A good plot is one that is well thought through. One that has things mentioned in the beginning that ties in to later parts of the series. Not one that seems like the author is just making up the series as she/he goes along. The best ones make you go back and say "oh, I get it all now". Well, this kind of thing is what I like about shounen manga too. Hmm, but In shoujo, I like their to be a good sustainable romance, one that feels like "they are meant for eachother". If a couple feels like they are fated to be together, I like the serious more. The shoujo manga that I tend to dislike are the ones where it feels like the main girl and guy could have fallen in love with anybody, meaning that they you could easily see them losing interest with eachother and getting together with someone else after the end of the series.
Well, I'm done now. I'm not sure how much of that you could understand.