Not with plugins. Plugins do almost all the math for you aside from pretty simple stuff.
The main things are calculating delta-v and thrust to weight ratio. You can get away with just putting a rocket together and see what happens but you really have no way of knowing if it will be optimal or get to where you want to go without doing the math first, but MechJeb can tell you your total delta-v and you can look up online the delta-v budget for all the planets and stuff, so that way you can know if your rocket will get there (or even off the ground at all) before you try to fly it and end up running out of fuel or crashing on the pad because TWR is too low in a stage.
Edit:
Given that though, after a while you can just know what works because it doesn't really change. So your ability to just estimate automatically increases with experience and eventually you don't have to do much math or really use the plugins a lot after you've done something a few times since you just remember what it took the last time.
Edit edit:
Protractor also tells you your required delta-v for each planet and moon and will give you a timer for when to burn to get the correct phase angle and actually get to the planet, and not be where it would have been two days ago and miss it totally.