We should never ever have ended up with two ways to render blocks in core.
It came about because we needed a better way to ensure block regions were rendered in order to finally put ourselves in a position to better solve issues around the display of block regions and to allow a simplier theme design be be established for example (look at how we simplified bootstrapbase/clean).

When that we done we "deprecated" the old blocks_for_region method however it was never given a debugging notice and core themes were not converted.

This MUST happen.
Really MUST MUST MUST happen.