Prog bands, in general, are not the best at leaving their mark on history. What we used to think of as big bands are today merely footnotes in old librarians collections.

Steven Wilson may have a shot imo...Radiohead too if one considers them prog (I don't). 

a) X band gets so big that history naturally spreads it's legs.

b) X band reinvents the wheel and adds to the genre something unequivocally new and unique.

I'm not sure that any recent band is original enough or has gotten enough attention to go deep into history.

Ones I would like to see do so are:

Jack O' the Clock

Godspeed You! Black Emporer

Miriodor

a? Are you saying if X band goes to the buffet religiously that it will get fat and only has to spread its legs?

b! this is the true meaning of innovation but these days not enough to get instantly recognized. I think that bands well buried in history will be resurrected and put in a new perspective as well as those lurking about now. i can think of quite a few totally original contemporary bands that are utterly disregarded in the now zone

Well that's a defeatist attitude if i've ever heard (or read) one. Music isn't TOO anything. True, the genres have produced more subgenres than ever before but it's not without some kind of regonizable guide as how to navigate the whole thing. In 20 years from now things won't be any different than they are now in respect to tracing historical paths that led to whateever came after. I mean, really, is something in 1996 so far in the past that we can't trace it anymore? Music is more exciting now than ever IMHO if you have the time to keep up with it all. Since music is my addiction i am living in the best time of humanity IMHO. Just my food for thought :)

UNREAL CITY has released 2 excellent albums already, they 2nd is very impressive (solid 5 stars).

If Il Tempio delle Clessidre will find a better singer they are able to make it as well.

It's clear that some think that certain bands will be remembered historically, but it's also clear that there isn't much of a group consensus that these bands are of that quality.   Maybe the force of prog rock slowed down because society around it slowed down.  That's just a personal choice, however, but when I listen to the pop music of the 60s and 70s, the feeling I get isn't really that different than the prog of that time.  But when I listen to the pop music of today, the feeling is very different. 

That said, the OP did add the caveat "like Dream Theater did in the 90s" which is a lower bar to set than what I initially thought the OP meant. I would say Godspeed and Battles were innovative but seemed to have missed their window. Sigur Ros, maybe. Deafheaven's controversial enough. Maaayyyybe Swans, though I think they've been more influential on the current post-punk resurgence. 

(Mike Portnoy has proclaimed their new one to be the best album he's ever been involved with - a cross between Tommy and The Wall. If true, then the Neal Morse Band will indeed make history.)

 

But on the reals - no current band has the kind of following the Big Six had back in the day so the correct answer is (unfortunately) none...

It's the same today, as it was yesterday, and 40 years ago. Nothing has changed except that in those days, some of us still had something in many colors and today we don't go around looking like clowns at 55 or 60.

Most of the music in the late 60's will be remembered as a part of the international events that brought about a lot of social change in many countries ... and the music, is now believed to be by many, an unifying factor, for its valuable content, feeling and humanity.

Most artistic scenes in any century, only last a few years and then dissipate. It is not usual for major art/music/literature scenes to last more than 20 years, even if the artist lives beyond that. He/she is still a representative of the time. 

For all intents and purposes, this would mean, in my estimation, that a lot of music in the 1990's, 2000's and 2010's might not exactly be remembered, unless the artist happens to continue working for 40 to 50 years, when the amount of work has a tendency to stand up and be counted. And this is the factor that a lot of material in the "lists" is not considering, when they are looking at preferences (as in an album!), rather than in an artist ... it makes for a popular contest, that I am not sure is going to be remembered in 75 years. 

However, including my writing here, a lot of this might end up getting swallowed by the media ... and how it behaves and shows itself in the next 50 years ... and if the commercial environment is still the control norm for most arts, the chances are that we will not have anything new for sometime yet ... and again, remember that most of the stuff that became known as "progressive" was not getting played in radio ... and it still got attention ... so we know it can be done.

I like to quote Guy Guden on this one ... when he was told that what he was playing was not rock'n'roll ... and he said ... who cares! It's great music .... and this is what you have to learn to say and believe in ... because the commercial side of things and its goons, is not going to go away ... you can hear them in every AM/FM station on the air! Or you can listen to them on Sirius/BS anytime! AND, they still don't "listen" to music, at all!

https://open.spotify.com/album/631K4FYqEZBjhFqk3xlF5k