The defensive transition was worse before. Slower and had one less midfielder to sustain pressure and retain possession. No system is without its flaws and 3-4-3 got its obvious ones on the flanks reliant on Neymar and Rafinha putting in a good defensive shift, but it's still working better than the 4-3-3. We just got to ride out this season this way somehow and hope for the best.
I don't think we'll get Dembele this summer. Maybe buy Bernardo Silva and play him as RW? Personally I would also bring back Deulofeu and see what he can do.
BTW, don't know if this is true but I've heard yesterday that Messi has scored 5 out of 6 penalties against Diego Alves. Given that Alves's save percentage of penalties against other players is around 50% that's great achievement.