As for the timer - I do have an auto-countdown timer. You set how long you want to rest between sets, and as soon as you enter one, it starts counting down. When it gets to 0, the phone vibrates. Is that what you're looking for? It also records the time, so if you don't follow the timer, you'll be able to see how far apart the sets were.
I have some semblence of what you're talking about with muscles and routines. You can create your own exercises if you don't like the presets, and add tags to them. Tags can be anything - muscle group, body part, etc. You can then search for exercises by tag to find specific things.
When creating a routine, you select an exercise list, and then have the option to add a week/multiweek schedule, where you say which day you do which exercise + expected reps/sets. If you did set a schedule, you can say what week it starts at (if its multiweek), and when you view the routine, it tells you what exercises you're supposed to do that day.
I'd like to eventually add some sort of animation or video to demonstrate the preset exercises. That's a lot of effort though, haha.