As in a completely new program from scratch, or? I severely doubt they'd do a new program unless you'd be able to transfer what you already have on there as well as being able to still use code cards.
That being said, since it's on the topic, I feel like I should mention I'd like to see them more actively update and improve the client however, I feel like there hasn't been any big updates since... Hell, four years ago now?
There had been, a year or so ago, some chatter about a new program from scratch. And yes, I think they very well could, just like how MtG did - especially now, with so many people being used to online play. PTCGO just has so much cruft, and it's impossible for them to make any money from it, even if they wanted to, the way it's currently done.
And transfer-wise: yes, it would suck, and they probably wouldn't allow you to transfer everything. But, MtG did it, and despite the groans, managed it pretty well all things considered from what I understand. It would be worth it for a modern game that was actually as good or better than in person...