If they only play the same songs from FII it's because the rest aren't that good
Joking aside, FII isn't a fan favorite album, so it's not really something they want to invest a lot of set time on. Still, like Max said, quite a few songs have made it to the set on the MM era, so we might see more pop up in future tours. I expect them to play Hollow Years and maybe LITS again at some point.
About NM played live again, I don't think that'll happen as this is what James said about it in 2011:
Here’s a question that a fan asked me to bring up: What are your favorite and least favorite songs to perform live?
Uuuuuh… Least favorite… I would say, probably… I don’t know… New Millennium. That song, I just didn’t feel it. There were some cool moments in it, I just didn’t… whenever we performed it, I didn’t feel it.
Source:
http://dreamtheater.club/blog/2011/07/11/resurfacing-an-interview-with-james-labrie/And I do recall a live online Q&A with DT around the time DT12 was released where Jordan was asked about two songs related to the previous two keyboardists (Eve - KM, and Anna Lee - DS) that hadn't been played since 98 and Jordan asnwered something along the lines of "if they haven't been played for that long, there might be a good reason for that", so no Anna Lee live either.
As for me, personally, I consider FII to be one of DT's weakest albums (ironically, the sound and production are almost perfect), but the good songs are really good, so I'd rather have them focus on those than try to play something like You Not Me or JLMB.