As weird as it sounds, I go onto eBay all the time and pick up Crestron gear for under $300 a unit. I can pick up wired touchpanels, new generation control systems (RF base stations!), and some remotes, like the MX-850 to integrate with it.
The learning curve is a real PITA, but once you start to get it, then you realize that you can really do everything.
The biggest issue, with all other brands, tends to be reliability. Because most work with lesser expensive RF pieces, and the brains are in the remote, there is no way to know if the receiver properly got 100% of the commands. That's the difference, because Crestron uses dumb remotes (no macros), but uses a control system (like a computer), it only receives one command. Basically, if you hit a button that says 'CABLE' - it can be programmed to check to see if the TV is on, if it is, then it just switches to the cable input (call it input 2). If the TV is off, then the system will first turn the TV on, it will wait until the TV warms up (8 seconds or so?) and then it will switch to input 2.
It works the same with all of your equipment, and only turns on what you need to use, not everything in one shot. Items without discrete on/off are a bit more difficult to deal with, but because you can program it, the reliability of non-discrete devices can be 99% reliable.
Is it better than Pronto? Hands down, yes! Is it more difficult to program? Once again, hands down, yes.
If you are up for a serious challenge, but want to reap the rewards, Crestron is a solid step ahead of almost anything else.
If you use the 9400, and you find that you are able to program it alright, but it doesn't meet your expectations, then you likely are ready for a control system instead of just a remote control.
In perspective, I've had programs which have controlled hundreds of inputs going to dozens of outputs, with full two way feedback and such nifty features as weather, shades control, full XM interactivity, full iPod interactivity, etc. It's not straightforward to PROGRAM - but using it truly is as easy as it gets.