All scrappers can do decently at the end game, but kat/sr will be more potent and able to pump out more dps than the ma/regen. Both can be made rather tough: you can soft cap the kat/sr and you can provide around 25% defense to the regen.
The Regen will be a click fest trying to stay alive. If you LIKE that, then you'd probably enjoy the combination, and Martial Arts won't have the redraw problems that a lot of sets have with Regeneration. Otherwise, I'd go Katana/Super Reflexes. It's fairly fire and forget, fairly strong, and Katana will prevent any "late blooming" arguments that people can have against Super Reflexes. End game, I think the Katana/Super Reflexes will be stronger.
"That's because Werner can't do maths." - BunnyAnomaly
"Four hours in, and I was no longer making mistakes, no longer detoggling. I was a machine." - Werner
Videos of Other Stupid Scrapper Tricks
Maybe swap the 2?
Katana/Regen or MA/SR
otherwise just go with what Fury and Werner said 
I really cant decide which to take, how do they fair at end game, cuz i can usually get past the early levels to appreciate how much a hard toon in low levels grow to very strong in the end...if i can get some pros and cons of each it would be amazing this toon is for PVE