Cradles are great for convenience -- so easy to use and no fiddling, but only one place to charge. Ports are great for versatility -- you just need a usb cable, and can charge anywhere. A personal choice.
One important thing to consider with any rechargeable option is whether the charger in question is safe to leave connected. Not all charging circuits are created equal, and some might not behave properly if left connect indefinitely. Many rechargeable things say in their instructions to remove the item from the charger after it's fully recharged.
I think that with an integrated charging port, people are more likely to unplug it when the light turns green (or whatever) so that the light is available for use.. whereas with a cradle the light sits in the cradle even after it is fully charged. If the solution involved leaving the light charging, I'd want to be convinced that the charging circuit did the right thing after a full charge (whatever that is. I'm not an EE.) I have a vague idea that more attention is being paid to this now, and more charging circuits are handling it correctly, but it's a good idea to read some reviews.
Regarding reliability of integrated ports, I would worry if it was a mini-usb port, but not micro-usb. The change from mini- to micro-usb supposedly moved the common failure point from the female port (ie: the device, hard to replace) to the male end (the cable, easy to replace). So if you're experiencing failures charging a micro-usb device, try a different cable. I can't find the reference that I'm looking for, but this is close
http://www.powerlet.com/learningCenter/usb-connectors
I don't think I'm a fan of the proprietary batteries for charging either (Olight S30RII or R20 Javelot for example). My dog door collar does the same thing; CR2430s are wrapped so that both poles are on one end of the cell making a battery replacement either a locked in purchase from one vendor or a crafting project to fix up a new cell. But.. I like the door
So I guess for the right light I'd probably do it anyway.
Those Olight SxxR lights have been calling me for a while now.