I went the URC route before moving to Harmony remotes. Harmony was much quicker and easier to set up. Unfortunately the newer MyHarmony site was flawed at introduction, and continues to be today. You can not enter discrete codes (or any custom code for that matter), and the new hub is limited to 8 devices. Moreover, there are just too many things you can't find a way to do.
Earlier this month I decided to try a Global Cache iTach. Initially with an inexpensive standalone mobile app. It worked marvelously. Not only with the mobile app, but I was finally able to control my IR gear via my home automation server through the use of scripts.
I have now moved on to iRule, and while not perfect with its clunky authoring interface, I have been able to accomplish everything that I set out to do, and more. And it will only get better.
Gone are the annoying activity based out of sync issues you had with harmony if you manually controlled devices, and my layouts are exactly the way I like them. I was initially concerned about not having hard button remotes, but since I have the freedom to set them up exactly as I use them, there is really only one concern (watching the TiVo and needing to skip commercials every 5-8 minutes). And I solved this by getting my unused TiVo remotes out of the old boxes.
So now I have two remotes on my end table. The TiVo, and either my phone, or tablet, or iPod. All of which serve to control lighting, 3 A/V systems, alarm and HVAC, all over wifi or cell data, from anywhere I have access to them. I couldn't be happier. The new iTach stuff is cheap, nicely made, and works incredibly well. I know iRule has no Windows Phone runtime at this point, but are you sure no one else has an IP remote solution. Also, might something like a dedicated Nexus 7 be a solution you would consider. Nice thing about the iTachs is they don't care what talks to them. I even wrote a little remote control program for my MacBook to control my office system. Anything that can open a socket and send a string over TCP will work.
Just my 2¢, but good luck with whatever you decide on!