I recommend the mx-3000 over the Pronto. If you never programmed a remote before its probably best to speak to a pro. They will give you the best answers and suggestions after they take a look at your set-up.
Do you know if your sources have discrete codes? Do you already have lighting control in the house? A pro will be able to integrate everything you want to do. If you want feedback on the remote from the AC to tell you the temp you are going to have to use a two way system like AMX or Crestron. you should also know that URC does not give the software to the customers any more. So you really need a pro to program it. You should also look into RTI. Its cost a little more, but its a great remote.
To find a pro go to Cedia and use the finder service. This is a place where you can find a list of pros in your area.
[Link: cedia.net]