Well, this is where everything really clicked. Play a few matches, add some points, play a few more.. ect (just like in the past) But you really start to feel what the mech is lacking, and move points into that area first.
One, you are not jadded on how the mech was before, because you never played it.
two, adding 5-8 points at a time, makes this far less overwhelming.
I leveled up 3 nova's the other day, (though one had master points, the other 2 didn't and the last is almost done. By mid way through the second mech, it all clicked. Now i'm onto my last, and know exactly what i need to add outside of a few random points i am wondering about.
I then jumped into my Warhawk and Dire..(yippy saved a ton of cash only buying one!) The warhawk i am not sure what to do first, but i'll play some more matches because i need to anyway for XP.. the Dire, well thank you PGI for that GXP bonus, because man that thing needed both sides of movement

But really all i am saying, If you really want to experience the new Skill trees, try playing something you never played before, it helped me really get the whole thing much faster. Perhaps it will help you as well.