EA likes its DRM, GOG doesn't. That's a big sticking point on System Shock 2.
Well, to be fair, we don't know that. We know that EA use DRM on their new games, but so do most companies here. There are several companies on GoG who have been known to use Starforce and Securom on their releases (not that I hold that against them, I'm pretty fed up with the the anti-DRM hysteria to be honest, I'm just pointing it out). So the fact that EA use DRM-solutions on their new releases doesn't have to be relevant here.
My guess, though it is only a guess, is that EA know their back catalogue is worth tons of money, and they're not yet convinced that they should "turn it over" to GoG. They have traditionally been very keen on maintaining control over their IP and products - they did not like Xbox Live to begin with, they wanted their own digital distribution platform instead of using existing ones like Steam, et.c. So basically, I think GoG will have to really prove itself before they will consider it.