I'm not thrilled with the idea of seeing prequel characters in the "VOTC" line either. I understand that the well of "main characters/army builders" might be running a little bit thin now with the OT, but I think that they could get another wave or two out of that series. I realize that the higher price stinks, but I have to say that the VOTC/VTSC have been my favorite part of the line since they first started out. Sure, they haven't all been perfect, but most have been pretty good - and the vintage packaging is just a spiffy bonus.
Like others, creating "vintage-like" packaging for prequel characters seems wrong. If they wanted to recreate the cards the figures/characters originally came on, that might be more acceptable - but like its been said, the regular line quality has basically come up to VOTC now, so they could just as well do these in the regular line. Also, sticking with the formula that they have used with the OT characters - many of the main characters from the prequels have been done pretty well (or will be coming shortly). Aside from maybe a few tweaks here and there, we already have nearly "ultimate" versions of Maul (Evolutions), Dooku (ROTS/Evolutions), Jango (Evolutions), Qui-Gon (Evolutions), Anakins (Evolutions), Obi-Wan Kenobi (ROTS and possibly upcoming figures that are now confirmed), Padme (Evolutions), SBD/Destroyer Droids (TAC), Palpatine (Evolutions), Clonetroopers (various lines), and the list goes on. Aside from a few changes (maybe adding in ball jointed elbow on some, paint differences on others), we're getting closer to getting an "ultimate" lineup from the prequels as well. That being the case, we'd basically be getting repacks for $10 each.
Just keep cranking out remaining figures like TPM/AOTC Obi-Wan, Jar Jar, more Padmes, a good Battle Droid and others in the basic line - and leave the VOTC line for the OT characters. There's still good versions of the main characters to be done for Han (Bespin), Luke (Hoth/Jedi), Leia (Hoth); army builders (Rebel Soldiers - all, TIE Pilot), or even miscellaneous characters (Gamorrean Guard, Zuckuss, Admiral Ackbar, etc.) I think there is at least enough left to make another wave or two. Finishing out the entire vintage run would be cool too, but seems unlikely.