It sounds like RF and wifi are nice to haves or are you hoping they provide more reliable button pushes or move devices to a cabinet? I guess I am asking if all the devices are easily hit by a decent IR based remote.

Adding RF always adds cost and complexity.

For wifi enabled Logitech just came out with the Smart Control that has a wifi base station with a very simple remote as the intent is that you will use one or more IOS and/or Android devices as remote control(s). This device runs $129. I have no experience but it seems to fit the bill on cost. Though some reviews around these have complained about lag on button presses, which makes sense since going over a network will take longer than a direct IR blast.

On the RF front I can share my experience with two devices.
I have all my equipment in a closet in another room so IR is not an option at all. For the last 5 years I have used the Harmony 890 with the RF Extender. It recently got to the point where too many buttons were no longer functional so I needed a replacement ASAP. I did a lot of research and I came down to either a Harmony or URC solution. I deliberated between getting another from eBay and new Harmony Ultimate, or moving to a URC MX-780 or MX-880 with an MRF260 RF base station. The URC Pro line is extremely expensive (MX-780 $299 and MX-880 $499, plus the MRF260 $249) so $550 or $750 retail, versus $350 for the Harmony. Then unless you can convince a retailer to provide you the URC programming software you will have to pay at least $100 for them to program it. They have cheaper options on the net, but they have no warranty and no one seems to provide the software. On eBay used URC devices can be had for less and usually included the software.

At the end of the day I decided to go with both used Harmony and URC. I got a very lightly used Harmony 890 for $107 that I basically plugged in and loaded my configuration on and after about 2 hours had everything working again.

I then got a used URC MX-880 and MRF-260 with software for $170. It took me a bit to learn how to setup and program the URC devices, but I got it working pretty well in my setup. Now we have his and hers remote controls in the living room. It is very apparent the difference between a consumer programmable and professional programmable remotes. The Harmony at least for my configuration was up and running faster. All my devices were in the Harmony online IR Database. The URC Database was missing or had incomplete codes for 3 of my devices. Ironically I ended up programming the URC with the Harmony and I will likely improve the Harmony by programming discrete on/off codes from the URC as I was able to paste in Pronto Hex codes from these forums.

I think once I have spent a bit time tweaking the urc MX-880 I will like it between than the Harmony. From a pure physical build quality the MX-880 looks like it will last much longer than the Harmony. The Harmony remotes have always felt cheap.

Hope this help to give an idea of what options there are for an RF solution.