Kuuga MethodMuch like Babylon 5, Masked Rider Kuuga was shot in HD, but because of technology and budget constraints, was edited in SD. And like Bablyon 5, they shot in HD so that, at some point in the future when editing in HD was less expensive, they could go back to the HD footage and make new HD masters. And again, much like Babylon 5, this has not yet been done.
Kuuga's video quality also suffers because the DVDs use analog NTSC-format masters that have horrible dot-crawl and rainbowing. Only the Special Edition DVD has footage sourced from the original digital masters, and it looks MUCH better.
Agito-Blade MethodChances are, someone at Toei figured it'd be better to just shoot in SD if they were going to edit in SD, and not letterbox anythung until you were making the broadcast masters. Plus, this let them use the wide-screen mode in the DVD release. While this means these shows could never exist in true HD, it let them have better masters at the time than they could using the Kuuga method. Toei finally went back to HD with Hibiki, which was shot, edited, and broadcast in 1080.