Regen or super reflexes for a Martial arts brawler
Regen is best IMO, but the main con is the level 16 armour, an essential, glows bright green, as do most powers 
Regen is probably better to try if you're starting out for the 1st time...good mez protection with added regen, 2 great heals, quick recovery (the power everyone wishes their build had) and Instant Healing (just simply Dang!) essentially its the safer choice.
Super Reflexes to me is the gamblers choice, there's no heal (altho you can take from the Medi pool for that)...so it all relies on luck, there will be times when you don't hit for ages...but at the same time, all it takes is a string of unlucky hits and you'll be eating dirt.
Both are great sets to play (my 1st scrapper was also MA/Rgn), but as i said Regen is the safer bet to start off with.
It is said that regen is the easiest starter for a 1st scrapper. I personally don't like regens because you have to check too often your health bar to click the heal, I prefer the toggles, click and forget.
Super Reflexes and Dark Armor have been improved a lot with the IO set bonuses and now SR is not a too gambling set as it was before, but still is to a certain degree, you will be very difficult to hit but when you will get hit, you will take ALL the dmg. Of course, there are ways to ease that, being Medicine Pool the most popular one.-
If it comes down just to regen or SR, I'd definitely recomend SR because is far more fun toon to play, but I'd also consider Invulnerability, quite easy going set, will breeze you until the 40's when you'll start having trouble with psionic dmg. Good news is that now, with IO set bonuses, it is not difficult to give an Inv scrapper around 20ish% psionic resistance.-
Ignore Nightmarer, SR is fun but not as fun as Regen! 
In all seriousness both sets are excellent, but as you've just started to play I'd probably recommend Regen as it is a much easier set to play and is more forgiving.
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In other words i was hoping to find out whether or not Martial arts is better or worse than regen or if they're both as good as each other what the pro's and con;s are when they're used with martial arts.
Any help would be appreciated.
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Well Id take Martial Arts over regen anyday. Using Martial Arts with Martial Arts, its one thing at a time, where as when using Martial Arts with Regen this isnt always the case.
Regen is basically a easy off of the bat type set, that easily can help any new person, to see the game with minimum downtime. You probably wont be playing the most challenging of characters to play in a team ie what maybe easy for you, isnt as easy for others, so have a thought of other players survivability.
He will honor his words; he will definitely carry out his actions. What he promises he will fulfill. He does not care about his bodily self, putting his life and death aside to come forward for another's troubled besiegement. He does not boast about his ability, or shamelessly extol his own virtues. - Sima Qian.
For a new player I think regen is the best as it's easy to plan when to take powers (no rush for stamina) and it as a very nice toggle for mezz protection and regen, i'm trying Dark armor now on my second scrapper which starts with some good resistant toggles but lacks healing until you get Dark regeneration.
I just started the game recently with a Martial arts Regen scrapper.
Being the mildly insecure individual i am and knowing very little about the game i was hoping to find out before i put a lot of time into the character whether or not this combination is a mistake or not.
In other words i was hoping to find out whether or not Martial arts is better or worse than regen, or if they're both as good as each other what the pro's and con;s are when they're used with martial arts.
Any help would be appreciated.