Yes, obviously he's more popular than Fujin. Plus, he's from the original MK cast. And while from that MK1 group of characters only Liu Kang and Goro didn't make it to MK5 (although storywise they're in), the rest in the number of 8 fighters (apart from the fact, that's not the same Sub-Zero) did make it. So Raiden, being clearly an iconic MK character, had to be in the long-awaited installment of the series as well.

And as regards the story, his presence in MKDA is coherently explained in his in-game bio:

The Elder Gods were fully aware of the potential damage the alliance between Quan Chi and Shang Tsung posed to the stability of the realms. Yet even with this foresight, they all stood firm on their decision not to interfere. All, that is, except for one...Raiden. The former God of Thunder pleaded with his fellow Elder Gods to take action, but they refused. Disgusted, Raiden relinquished his Elder God status and returned to Earthrealm to gather support against the coming storm.

Raiden returned to Earthrealm to reunite with his comrades and inform them of the impending threat from the Deadly Alliance. Those that accepted his call to arms were instructed to meet him on Shang Tsung's old island fortress, located in the Lost Sea. Once there, Raiden explained in detail the dire situation that faced not only Outworld, but Earthrealm as well. He then summoned Shang Tsung's Nethership from the ocean depths and with it transported them all to a celestial portal known only to sorcerers and deities. They emerged in Outworld ready for battle.