Passive early, OP late. I see no real difference. Even without her Q, which was never much of a burst to begin with, rather pretty much sustained damage, her kit refuses to make her unviable, even in laning phase. Just by building a chalice and guise at the same time, you've easily made up for the mana increase, and all that's happened is it takes a little more time to build your next item.
Besides, I jungle Elise. Currently Twisted Treeline is dominated by bruisers, and if there are no strong AP champions on the team, naturally they will begin to stack armor opposed to magic resist. Because of this, early game I focus on becoming tanky. I'm not too much of an asset to my team early damage wise, but my kit still allows me to bring in just as many kills. Then--when I decide the right moment, I begin building my strong mpen items, like blackfire torch, and out of nowhere, I have an incredible burst, sustained mana, and am still tanky. All that happens is it takes a while longer to become a scary threat.
Because I main her as a jungle, it gives me room to recall all the time. I really don't see any viability issues with her, maybe just a change in playstyle.