Using PADS means relying on myepisodes, but it's big advantage is that you don't need to set anything up (if you alreaduy use myepisodes), in my opinion.
The other options you mention are the biggies
Episode Butler is stable. Works well. You just need to add your shows once and it's pretty set and forget. It's very simple to use.
Media Rover admittedly pretty hard to setup if you aren't familiar with configuration files.
It's a great set and forget solution (moreso than the others, even).
Media Rover will figure out which shows you're watching automatically after you input your TV directory. As it is run it looks at your TV folder and makes decisions on what to download or ignore as it parses the RSS feeds you give it (you schedule it to run periodically).
This means if you start watching a new series MR will notice by itself because there is no static list of shows you're watching. It's dynamic according to your file structure at the time media rover is ran.
So it figures out what series you're watching based on the folder, and it does the same for episodes. Media Rover simply decides not to get an episode if it already exists on disk. It also checks your queue and nzb backup directory to prevent dupe downloads.
The simple intelligence Media Rover has by checking for the presence of files is great, and that is it's biggest feature for me.
The other rather big, unique feature of Media Rover is that it has support for RSS feeds from several different websites. You can use them all if you want. Maximise your chances of getting the right episode, faster
Another part of MR is it's renaming script that renames and re-organises your downloaded episodes into their rightful format and place.
The only big con some people might find with Media Rover is it's inability (at the moment, anyway) to recognise SD content or HD content.
Also, in good development (though i haven't been following very closely) is sickbeard, but I don't think it's quite stable yet for real use.
This is just my 2c on some of the available options, but the best bet would be to do further research yourself.
Personally (as I'm sure you guessed!) I like Media Rover. It's very 'complete' in it's features. Development isn't super-quick at the moment but Kierse has done a great job so far and it's very stable.
Good luck
