Honestly it depends on the author. Basara and 7 Seeds, shoujo and josei respectively, are two of my favorite manga and are written by the same author. I've loved and hated titles from both genres. Most of the hate is geared towards cliches like "plain/ tsundere girl going out with hottest (jerk of a) guy in school" or "ultra rich ultra hot (ultra conceited) company president falls for regular gal with low self-confidence".
Every time I find myself leaning towards josei I chance upon an awesome shoujo like Meteor Methuselah that combines mature themes with a great plot. Every time I find myself leaning towards shoujo, a slice of life josei like Kuragehime comes along and I'm stuck between the two genres again. I've been reading manga for about 5 years now and my tastes have changed a lot- before I could read and like just about any romance or action, but now I prefer plot and character depth over such things. But even though josei are now tipping the scales when it comes to my favorite manga, I can't say it's my favorite between the two because I believe the quality of a story depends on the author, not the genre it's been dumped in.