Lr5 didn't see much, if any change in this area. However, the recently released 5.2 update has undergone a bit of work to address the worst excesses of auto tone. I think it would be worthwhile downloading a copy for the 30 day trial period to see of it helps in your situation.
Details of where to find the download and some discussion of auto tone can be found in the Lr team Blog at http://blogs.adobe.com/lightroomjournal/2013/09/lightroom-5-2-now-available.html
Message was edited by: Ian Lyons Fixed typos
Lr5.2 is better - try it!
Auto-tone in LR5.2 is now useable as a starting point for way more photos than is was pre-5.2. Good job Adobe.
Thank you everyone - I did give it a try with 5.2 - and it actually became usable now.
Got the update and I'm happy again. Thank you!