Finding better routes than bicycle apps suggest
This is an impossible question for the mapping sites to answer. They come up with heuristics about what makes a good route, that will do a pretty good job, but there is fine detail they do not and cannot know. For example, Your route 2 is the easiest on paper, but what if it poorly sealed with course chip and has lots of rubbish and stones in the shoulder. Route 1 has been recently sealed with smooth, fast hot top and has a wide clean shoulder. Route 1 would be better. What if route 2, getting onto the top of the ridge exposed you to a prevailing head wind that route 1 was sheltered from - in this case the best route changes daily (Where I live, hourly). 

Add to this, a good route is subjective - as already suggested by @bibz guys out for training rides have different definition of good to a commuter. As a MTBer, I have a different definition of good to a roadie, as I have much lower gearing I can climb steep hills roadies want to avoid, I careless about gravel roads, road works or poorly maintained roads than roadies. They tend to want to go faster (and further) then I do. I am a strong hill climber, and will take a hilly route over a flat route any day, there are many who hate hills and a much stronger than me on the flat. (TBH The vast majority who are stronger than me everywhere). 

In the end technology cannot make you decisions for you, all it can do is make suggestions based on the data it has. Ask around locals for better advise, but in the end you have to actually ride the routes to work out which is best for you.