There is a fine line that needs to be looked at before you commit to Prodigy.

Prodigy is a great system actually (The stuff that is availiable anyway).
+Remote access via Econtrol for Lights,HVAC,Security,A/V,Etc.
+Low cost solution that does a lot more than anything else in it's price range
+Expandable
+Fully programmable via Simpl/Vt-Proe
+Two way communication to PLX-2's for cheap

- Only has 2 com ports
- Only expandable to 3 Tstats, 6 PLX-2's, 1 Idoc, etc.
- Only compatible with Prodigy equipment

If you want a TPMC-8x, TPS-6, multiple Idoc's or countless other regular line Crestron products then a Prodigy won't work.

As far as control of a Niles, I don't see a module for it. If you have the protocol for it, then you should be able to program the Prodigy to run it 2 way.

When you say the Pro App, I assume you mean the iPhone Crestron app. I have not used it on a Prodigy, So I can't really comment on that. It works fine with a regular Crestron system once you get through all the setup.