Since this arose (after upgrading to OSX 10.12.2 a few days ago) I too have tried everything advised here, including the rebuilding, reindexing, PRAM zap, and changing the settings in Trusteer - to no avail.
From a different forum, I tried starting in "safe mode" (gotta love that screen flickering!) which did solve the problem... until about 2 minutes after the next normal reboot. That implies that the issue is another process interfering with Mail.
By disabling Trusteer entirely (clicking "Stop Rapport" and going through the convoluted authorisation process), I got the problem to go away. At least in my case, the issue is having Trusteer running when Mail is launched.
In reporting this to Rapport's makers, an outfit called IBM, I noticed that Rapport updates itself in the background by default, which may explain some other users' experience of significant performance changes occurring despite their having made no conscious updates. I'd like to suggest to Apple that any time an installed application makes an update, the system could pop up a message to confirm that this has occurred, and offer a simple route to reverse the update.
Meanwhile, hooray! I can see my email. Including the latest invoice from Apple. Hooray!
The compliments of the season to you all...