I'll hazard a guess and say yes, it will be more popular. I've read that the paint job is largely loathed, based on production photos and early, pre-release comments. However, I am seeing most people's comments once they have the ship in hand, are fairly positive.
Couple the positive comments with the relative scarcity of the first release and I think it will move, if only because people can pick up a packaged Y-wing at retail prices. Add the improved packaging and you have a number of factors that should lead to good sales.
Vader's Tie, on the other hand, was never really difficult to get. I managed to pick one up at an online retailer years after it's initial release and year's after they had ceased to be seen on shelves. It was easy to find and not at an elevated price, so anyone that wanted one probably picked it up. Only packaging fans would snag this version. People like me that like the packaging but already own one are patiently waiting for the clearance pricing.
The pack in figure may influence it too. Granted the Y-wing pilot is nothing overly spectacular, but it's not as common as a Vader figure, of which there are no less than four versions currently available at retail right now (with some variability in availability of course). Easy enough to modify gold leader, sure, but at least it's a tiny bit different, isn't it?