KMail1 had its own internal database, KMail2 re-uses MySQL. I guess MySQL, which is after all a more generic database, is not as fast as the internal database of KMail1 was.
There are probably also still quite some opportunities for performance improvements since much of this is new while KMail1 had been optimized for years.
But essentially, there is no difference in KMail1 and KMail2 except that the backend of KMail1 is abstracted out and uses MySQL (or other backends, they are plugins after all) instead of a home-brewn solution.
Sounds like an improvement to me. I am very much aware that currently, it doesn't feel like that with the stability and esp performance issues and all, but a change for the good often consists of one step backwards, two steps forwards.