The cIOSes have been updated recently.
Waninkoko has been more active, he has setup a twitter account where you can follow his developments.
cIOS249/250 is at rev17, and fully fixes error 001 and Dual Layer probs, and has support for the new "BCA protection present in New Super Mario Bros. Wii, but you have to insert the BCA data into the ISO first... Most USB loaders will do this for you.
cIOS222/232/224 has been updated, with several improvements. I haven't looked into IOS222 much, but it has FAT support, and v5 has a form of NAND emulation, and can save game save files directly to SD card.
And SNEEK (v2), the NAND emulator, is finally out. It can emulate the entire NAND flash filesystem from an SD card.
Preloader has been discontinued, but has been picked up, and it's now priiloader, which has several improvements.
Configurable USB loader has NTFS support, when using Hermes' cIOSes!
And cIOSCORP is now at version 3.6, and no longer stops hackmii installer, and it has Korean Game support for all Wiis.
And Nintendo has released New Super mario Bros. Wii with new Anti-Piracy stuff (as mentioned above), but the AP was foiled, just like everything else they have tried.
But not long before that, Nintendo released System Menu 4.2 Update. this is almost exactly like 4.1, except it tries to kill the HBC, and cIOSes (222, 223, 249, 250). It also has an enhanced region lock which stops modchips' region free ability. It also searches for channels with ID "HAXX" and "DVDX", and deletes them on every boot. Of course Team Twiizers have changed the IDs of said channels. The cIOSes get replaced with useless stubs, which can be removed with AnyTitleDeleter.
And 4.2 intentionally bricks Korean region-changed Wiis. And it will also try to update/overwrite you boot2 (if it's version is lower than v4), meaning if you have bootmii as boot2, and it's not already v4, it will remove bootmii! (but you can reinstall it fine though)
HBC is also capable of hotswapping devices too. No need to reload HBC every time you eject your SD, UBS, or SD gecko.
And since 4.2 was released, many apps have been updated to work with 4.2 and it's new set of IOS.
And there are several other improvements too, but I don't know every one of them, since I only use certain apps.
But no, you still cannot play IOS reloading games via USB. You'll have to use the alt-dol method.