Well Energy Melee has higher damage attacks and a slightly less resisted damage type (energy, though still mixed with smashing), and the secondary effects are all disorients.
Martial Arts is all smashing damage but you get a wider range of effect types, from disorient to knockback and even an immobilise.
If you want to scrap a bit after your assassinate I'd say MA because it will be easier to get an attack chain with decent ongoing damage-per-second, but EM is better for quick hit-and-run kills (especially in PvP) because of the amount of damage you can frontload on top of your assassinate with its higher level attacks.
Nrg is the best, MA looks better though.
50s
controllers: Ill rad , grav rad, fire kin, ice kin
blaster: ice em
scrapper: spines sr
I don't think there is really much to choose between them, they are both good, pick wichever suits your concept best and you like the look of.
I really should do something about this signature.
Energy and Martial Arts are pretty similar but there is one trick in MA worth mentioning. The high-end Energy atatcks don't do criticals. This doesn't matter if you use them as a follow up to your AS, but with Martial Arts you can do AS -> Placate -> Eagle's Claw and do a disgusting amount of damage that Energy can't match.
Still, I generally prefer Energy, and use Build Up -> AS -> Energy Transfer -> (General Melee while AS recharges) -> AS.
Get Martial Arts. If u want Energy make a brute 
Energy and MA are both ace. My advice would be to go with whatever set you like the look of, or fits your concept best.
The Smoking Demon
Ash/Tar Corruptor
Union
@The Smoking Demon
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Energy and Martial Arts are pretty similar but there is one trick in MA worth mentioning. The high-end Energy atatcks don't do criticals. This doesn't matter if you use them as a follow up to your AS, but with Martial Arts you can do AS -> Placate -> Eagle's Claw and do a disgusting amount of damage that Energy can't match.
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Energy Transfer (brawl index 12.66) is the only EM attack that can't crit (if you use it from hide it just doesn't drain 10% health from the user, like it normally does). EM's final attack Total Focus (brawl index 9.89) can still crit and it does more damage than MA's Eagle's Claw (brawl index 6.33).
The most "disgusting" amount of damage any stalker can do is an EM Stalker that uses Build-Up, AS, Energy Transfer, Placate then Total Focus - if you're quick enough (no gaps between attacks) then the build-up should last just long enough to cover the Total Focus. So if the OP only cares about frontloaded damage then he has to choose EM.
Im planning to make a Stalker but I cant choose between Martial Arts or Energy Melee. Which one is easier/better?