I've had a play with the 9400 and 9600 ProntoEdit, and it really is just as easy. There are more options in the "Action" for buttons (since it can do more) but it still contains jumps, links etc. that the NG version does. If I remember correctly, the system properties can be applied to all devices by default (so hard buttons have common functions) but can be specified per device if needed. I don't remember the NG version doing this, but could be wrong.
The one thing I did find it missed - the NG version allows you to use the colour at the upper left corner of a graphic as transparency colour - the 9400 / 9600 versions don't. Which is a pain since I only had Paint for modifying graphics buttons. But I've now bought a proper graphics package so it's no longer an issue.
As far as I can see, if you can program the 990 you will have no problems with the 9400 / 9600. They are just the same and I expect no problems at all.
From the sytem files on RemoteCentral, it looks like you can definitely fit more useable buttons on the screen. For my TV screen I have 3 channel buttons on each row - the 9600 configs seem to manage about 8 buttons per row fairly comfortably.