I'm also pretty peeved at the job they did with a lot of the cries of older Pokemon. What the heck happened to Loudred? It sounds like a weird.. squirt noise. Raticate sounds like a short scream. Oddish... that's really messed up. Pretty sure Aggron doesn't sound as cool, but I can't remember. There are more, but none come to mind at the moment.
There are some I don't mind, like Weedle's or Psyduck's. Still wish they would have kept the old ones. I was able to identify Pokemon from their cries alone, but now I can't with a lot of them....
I'm with you here, 6th Gen updated the cries to the new technology that the 3DS came with, but most of the time it produced such badly distorted results. I still can't get over how badly Dugtrio, Sableye, Gothitelle, Karrablast and a couple of others were ruined in the cry department.