Note: Keep Forge and Reconstruction maxed at all times.
Try to keep Focus at 52 unless you have a lot of gems. 52 is plenty to finish most dungeons and get all of the wild gem's boost with only 1 increased pool (Not the violent explosions boosted one)
Max Recharge, get Resonance to 20 as soon as possible, 65 when you can.
Max Radiance only if you are looking to clear, not for endurance.
Replenish should be gotten to 50 as soon as you can, but don't worry if you take points out of this to cover other skills. That is fine.
Jonny mentioned quite a few of the best masteries and I wanted to put in my own comments here for the best imo:
-Forge and Construction are no brainers.
-Triple Gem and Dual Gem are great boosters. Triple helps with L/Y/O and L/Y/R cannons, Dual helps mana farms with L/O and C/B traps.
Resonance is great to have as well as Recharge. Radiance is good however. You don't want you cannon firing into your mana farm.
Most Masteries except C and B are good. When you get to a point in farming in endurance where a C/B trap gem is 50000% slow and 40000% shock, there's little need to up them more.
Wild Gem means more mana, Flexibility means easier gem unlocks and faster 2x early.
Violent explosions means more monsters from summons and more mana out of wild gem.
Deadly is great for L/O farm
For those playing on premium, one of the biggest things to start with is rush to the first pylon, using increased Banish cost and heal when you do it. Set it to Armored, and play through like you normally would. Do not summon recklessly and charge the pylon early. Don't worry about battle amulets at first because you'll return to it and do it again later for more exp. When you are nearing 9000, spam grade 2 gem bombs (You should easily be able to cap out the gems you have) several times and gem bomb the farthest wave you can. You don't have to summon it, but get it as close to your Armored Monsters Kill Count as possible WITHOUT going over it or equaling it. This'll max out your summon multiplier and will get you 100k exp on the first run without too much effort. From there you can go back and do other levels with much more exp.