bigfred 

Not sure if you're asking about "wide" flanges or "tall" flanges. But, in both cases, they offer a theoretical advantage by providing a greater bracing angle to the spokes. However, in practical application I believe most have found that the actually angular change is pretty miniscule and the actual required spoke tension doesn't change much, if at all. I suspect that flange width from hub center line is more of a concern than flange height.

There are some hubs that are known to have particularly narrow flange widths from from centerline and subsequently not build up as strong a rear wheel. I'm not versed in all of them, but, I believe American Classic is amongst them. Can't tell you the rest.

Bearing design is another consideration. The classic shimano hubs that so many use, rely on open cup and cone bearings. These are almost infintely adjustable, but, rely on some periodic maintenance. White Industries and Chris King hubs utilize sealed cartrige bearings which don't require regular maintance but must be replaced once worn.

Of concern to me, but, it seems not many others, is freehub design and material. In the distant past I had a number of issues with both freewheels and freehubs. I've both stripped the ratchets and pawls and had them subsequently lock up tight or completely fail to engage. Whilst I've suffered this with both steel and alloy components the alloy ones where by far the less reliable. Subsequently, I ensure I ride with steel freehubs of generally reliable reputation. Granted, I've not ridden many modern alloy or ti freehubs. But, in the one instance that I leased a new specialized trail bike for a demo, it's light weight alloy freehub locked up on me and left me doing a little over 8kms of technical trails in fixed gear mode while attempting to not tear the deraileur off the thing. (I wasn't happy or impressed!)