Here's what I want in a remote:
o RF capability
o Rechargeable battery
o Powerful programming

The harmony series looks like a candidate in all areas except perhaps the last; I can't get a good handle on how exactly it's programmed. The how doesn't concern me as much as the what: I don't really care if the interface is easy or hard or requires me to learn a new programming language as long as I can get the device to do what I want. That could include a sequence of "activities" that includes inserting arbitrary delays (e.g., having to wait 45 seconds for a device to power on -- I know there are different delays in the harmony programming, but it's not clear I can insert an arbitrary one after turning on a device in one activity, but not insert the delay after turning on the device in another activity).

It could also include conditional statements (e.g., if its after 8:00 pm, do X else Y -- I guess that also requires a system clock, which may be pushing my luck).

Any recommendations?

Look into the URC line of remotes

MX900, 950, 1000, 3000 and a RF base unit...MRF300 or 350 or go big with a MSC400
www.universalremotes.com

Also look at the Nevo SL and its wifi based base unit
www.mynevo.com

There is also RTI, a T2C or T3 are awsome remotes coupled with a RP-6 and RM433. Only drawback is they are a dealer only item and software isnt available to consumers
www.rticorp.com

Not sure if the above remotes will offer the timing functions like you are asking, you might need to step up to AMX or crestron for that

If you don't need to spend a ton of money on this, any JP1 compatible "One For All" remote can do everything you need, including the delay. If you need the RF capability too, you would need a remote like the URC-9910 or URC-9964.

Note: any universal remote with RF will not work RF-controlled devices, the RF feature is just there to extend the range of the remote (ie, you can use it from another room). If you need to control an RF device, a universal remote won't work for you.

To give you an idea of the cost involved, I could sell you a URC-9910 (8 device learning remote with LCD screen) for $29 and a parallel JP1 cable for $15 (USB cables are $35). Plus $5 for shipping.

If you're handy with a soldering iron, you could easily make your own JP1 cable.

As for the rechargable batteries, you can buy those anywhere.