I've been through quite a few remotes, lol.
I started with a Harmony 650 in the HT and 300 for the bedroom. I then upgrade to the Harmony One and eventually a Harmony Touch because my One's LCD screen broke. The Harmony One is probably my favorite Universal remote out of them all. I loved the build quality and the button layout.
It one huge major flaw though (as all Harmony remotes do), lag/delay. Harmony Remotes have the worst lag/delay when trying to use Kodi or WMC!! Some people don't notice it because they've never used a proper MCE remote. I can literally hit the up/down button like 20 times and because there is such a delay, I can just sit there and watch the remote spitting out codes for 20 seconds and the screen move. I did all the delay and repeat tricks, but to no avail. It's a commonly known issue with Harmony and their forum has a bunch of post about it. I couldn't live with it and untimely left the Touch in the drawer and got an:
Inteset INT-422 - No-Frills Universal Remote that just works! Well, it did for 8 months and then died. Ugh. I did like the remote though and it was easy enough to use.
My fav non-universal remote though is this type. Ortek Media Center MCE PC Remote Control. That's what Amazon calls it, but I know there are several varieties. This replaced the Harmony 300 in my bedroom. Two problems, it's not back lit and it's not universal. But as far as HTPC functionality? It flat out works and it's amazingly quick. I can hit the button 20 times and it instantly moves the page with no lag or delay. It's AMAZING. But there's a reason why it's in my bedroom and not my HT.
So with that, last week I finally ordered an URC MX-890 remote. It's a bit trickier, but far more customization than the Harmony. URC also doesn't give out the software to end users. They are sold only to approved dealers. I got mine from a Dealer who was willing to give me the software and the remote was about 1/2 MSRP. I couldn't pass it up. I'm in the middle of programming it and will have it ready over the weekend. I just haven't had time this week and I need to control lights, projector, TV, HTPC, amps and a few other things. So it takes time programming, but right now it seems, far and away, a much better remote than Harmony. It's just not end-user dumbed down friendly.
In the end, if you're willing to drop the money on a URC, it's the best remote for a home theater.
EDIT: Oh, I also did the whole iRule and iPad thing. Hated it since it didn't have hard buttons and you have to look at everything. I think it would be cool to use as an entrance piece, like some sort of in-wall device at your theater entrance to turn specific things on. But not for everyday use.