I can give you a reason why Stacking is bad. For the last two days Comcast has been sending me a very stuttery, pixelated image on its channels. If the guide has overwritten my OTA channel information with Comcast equivalents for my locals I can pick the version of the broadcasts that is working. Also in general for locals OTA is just almost always a better picture, much less compression etc.
Now, the question is how do you get to not be stacked so your OTA is OTA and Cable is Cable. Very tricky. I have done it a couple of times but I could not talk anyone through nor can I do it reliably. I had to find out the hard way that clearing the library, clears the guide. That some crap. I have an OTA channel 2.1 the is like channel 34 on OTA and cable is something like 670. When cable has overwritten the OTA information than I get the right channel from Comcast but the guide information is crazy. I don't know what channel the guide data is for but instead of the local NBC affiliate data I get a bunch of car shows. If you click on one you will get the local affiliate via Comcast.
Anyway, it is tedious and you have to run load program guide, OTA first and then load the program guide for Cable provider and keep existing so it doesn't overwrite the OTA data however, it works correctly only rarely so I have had to do it over and over at times. It was really annoying that clearing the main library wipes the program guide information. TV needs to work like an appliance. I have sometimes had to go through it a half-dozen times only to not get it work right and just gave up for a week and went back to it and had it work the first time.
The whole thing is very annoying.