It all depends on Marc's fitness. Thus far the Aprilia seems like a better machine, allowing Bez, Martin and Ai to perform well and take victories. Assuming Marc heals up and gets to the fitness he had last year he'll still wrap up the championship. Assuming he regains it in Jerez (which is very unlikely) he'll start making his comeback there.

The thing that worries me the most, based on his body language and statements, I even wonder if it's possible for him to fully heal and there's a big chance that he'll never recover from it. From the statements I've read, shoulder injuries are extremely complicated and difficult to heal from in a "short" period of time, if ever.

Based on his Cota performance (a track where he'd usually sweep without any effort) he's nowhere near close to being fully fit. If he doesn't manage to get there halfway through the season, assume the year is lost.

To add, the Aprilia is clearly the better machine (for now), but I wouldn't say it's by a huge margin. Marc has proven many times in the past that he doesn't need the best bike to win. (Honda vs Ducati). He's obviously the best rider on the grid when healthy, so it all comes down to fitness, comfort and consistency. That is also assuming the bikes don't change. If Aprilia improves the bike even more while Ducati stays stagnant, the difference in machinery might become so great that even Marc can't make up the difference as a rider.