Yeah, agreed, I pretty much navigate my library by Search, Kobo or Kindle, and it's infinitely easier to deal with

. It's faster on both ends: nothing to maintain on Calibre's side, and much, much, much easier & faster to deal with on the device.
Granted, the saner metadata handling of the Kobo helps here.
(I still spend a few seconds cleaning up tags and setting up a "main" category tag (which I flag with a distinct prefix, in my case, a +, a remnant of my Kindle Collections setup), but it's now mainly because otherwise an endless list of tags in Calibre annoys me ;p).
Also has the advantage of not bogging down the reader, because neither Amazon nor Kobo has a terribly efficient collection implementation...