The Linux kernel already supports directly managing Flash without a controller. The JFFS2 filesystem is designed to run directly on top of the Flash device. This is used in most routers and other small Linux devices in order to keep costs down.
There's also f2fs [1][2], which has a similar design but runs on flash devices with an FTL and thus takes a more middle road. It still has a log structure and tries to make things easy for the FTL by doing large, sequential, out-of-place writes whenever possible, but it takes advantage of the FTL when it makes things simpler, like for certain metadata that's easier to update as a small random write.
It is interesting to note the design trend in mobile devices like phones.
Years ago, it was typical to have a NAND flash controller built into the SoC (like a TI OMAP, Freescale i.MX series or similar).
This is raw Flash memory, and it is up to the SoC plus OS to manage error recovery, remapping bad sectors, etc.
However, in recent years, most mobile devices just use one of their SD interfaces (often 8-bit these days) to access an eMMC chip. This looks just like a SD card, because it has a FTL in it which takes care of a lot of the low level details needed for Flash management.
Some SoCs these days don't even include a NAND Flash controller anymore.
