I really like the new standard shader and how easy it is to work with, but I am wondering what to do with all the older assets I have from the asset store that still use the legacy shaders. What is the best option? Leave them as is or change them all to the new shader? I have noticed some color fading if I do so - which sometimes actually looks better - but I am not sure if I should be doing this? Will I run into issues if I leave the assets as is with their legacy shaders until such time as the author (maybe) updates their work?
Use what looks best for now.
You shouldn’t run into any issues in the near future, Unity 5 will have legacy shader support.
I’ve found the Standard shader to have poor performance on low end mobile devices, so something else to consider too.
Thanks 
Mobile is not my target platform - good to know I can use whichever looks best at this time.