As both of my Pronto TS-1000s are dying, would an Ebay TSU-6000 be a smart choice as a replacement? ( I already know how to use Pronto Edit) Or should I bite the bullet and go for a Harmony Touch or something like that?

I have a 5 component home theater and it needs to be as simple as possible (like I have set up the TS-1000) for my remote-challenged (but wonderful) wife.

To each his own, but being a long time Pronto owner myself I'd suggest purchasing another Pronto. Rather than a TSU-6000 I'd suggest at the very least a TSU7500 such as the one listed here for example which comes with the RFX6500 extender as well though to be honest for just a few hundred dollars if you are patient you can score a TSU9600, a significant upgrade from the TSU7500, the initial release of the editor PEP v1 still retaining the same basic structure, layout and functionality as you are already familiar with in Pronto Edit while at the same time offering the majority of the advanced features the later versions of PEP provide. Of course there are current solutions out there offered by other manufacturers which could meet your needs, but none of them in my opinion are going to offer the overall value and programming experience that sticking with a Pronto will provide.