Yeah, Casio has some great hardware in these new CTX keyboards, but like you said, the user interface is confounding. As I previously wrote in another thread, while I was experimenting with a CTX keyboard (either the 3000 or 5000; don't remember which one), I came up with a cool piano/string type sound, but when I was done, I had little idea as to how I got to that sound!
Also remember that, while the CTX-3000 and 5000 have a 17-track sequencer, on 16 of those tracks, you can only record one voice at a time. And by that, I don't mean that you are limited to monophonic play (as you can still play and record chords), but that if you combined two voices with "Upper1" and "Upper2", it will only record you playing the "Upper1" voice. It would be like setting up a complex sound using the Main and Dual voices of a PSR-E400 series keyboard, but only being able to record yourself playing the Main voice. Of course, with the PSR-E400 series sequencers, that is not the case -- you can have a sound made up of a Main and a Dual voice and when you record to any of the five melody tracks, you will get the full sound of the Main and Dual voices combined, as long as there is enough available polyphony.
Who knows? Maybe Yamaha will start taking these keyboards in a different direction, as they have already kind of branched out with that PSR-E360. With the competition offering things like portamento, directly editable and storable sounds, and a more advanced rhythm/style section, they may realize that they have to up the ante on the newer models. I just hope they don't take away the live-control knobs and mess up the user interface in the process.