Could they clone Protheans, for future games

She'll clone Javik and imprint it with the mind she tentacled from Shepard.

Why would they? A clone doesn't get the same mind or memories of the person they're cloned from. While their bodies are Prothean, they wouldn't have the same mindset since they would grow up with our cycle's culture instead of theirs. And even if you try to imprint them with the old mindset, they could just refuse it like Grunt did. 

All they'd have to do is pickup Javik's soldier log thing, and instantly the cloned prothean would be aware of their history.  Not to mention that if they physically touch literally anything in any room and learn more about it than any of the other races, save maybe the Leviathan.  Grunt had a predisposition towards violence, just like most krogan.  And let's not forget about the naturally hostile behavior of the yahg.  I imagine protheans have a similar desire to dominate others.  If all else I could see a new shadow broker like figure being prothean. 

Did we play the same series??  The protheans can learn complicated thought processes by touch.  They'd be able to build a shadow broker rivaling network in a day. 

What would be the point? The clones won't be able to build a population without resulting to clone incest (that's if you are able to create female protheans from that DNA).

DNA decays during ones lifespan, so after 50,000 years, that DNA would be corrupted.

What of the XY chromosomes? Javik is a male so unless you are planning on making protheans with both male and female parts, you'd need something that shares a close kinship with the protheans (like humans with chimpanzees).

I feel the same way. The more I think about it, the less I see a possibility for Javik to make a cameo in the next Mass Effect:

From what I gather the next ME will be set after the Trilogy and after Andromeda,

Andromeda was set 600 years after the Trilogy,

The lifespan of Prothean is never explicitly specificied, though by talking with Javik in ME3 we can deduce that they don't live as long the Asari,

Now cloning aside, the only way Javik could make it out alive is by hitting a stasis pod again ^^. But it might feel like an overused trope at this point. 

But hey, I'm confident writers at Bioware could come up with a wild explanation if they really wanted to make Javik come back. ^^

I like Javik. On my first playthrough, I benched him because I was turned off by his dickish banter. But on my next game I finally took the time to listen to him.