There's a time and a place to deal with personal issues. An all-out alien invasion, is not one of them. There's a reason why there aren't any crossovers between Twilight and War of the Worlds. One conflict just does not accommodate the other. It's like trying to throw a fancy dinner party and a paintball tournament at the same time. It just doesn't work. However, this is often what Superman and Wonder Woman have had to do over the course of their relationship.
Throughout this series, which has created a strong narrative around a blossoming relationship, Superman and Wonder Woman do set time aside to develop their relationship, as all healthy couples do. It has led to many strong, intimate moments in between battles against gods, aliens, and everything in between. Whereas most couples have a hard time planning their private time around work and football games, these two have to find that time when a new global threat seems to enter the picture at least twice a month. Because of this, they often have to multitask between being two of Earth's most powerful heroes and being in a mature relationship. In the Superman/Wonder Woman Annual #1, their capacity to multitasking is tested in a big way and they don't necessarily pass with flying colors.
For most of the Superman/Wonder Woman series, DC's de-facto power couple have been able to achieve a consistent balance between dealing with threats and growing together as a couple. In the same way that couples who play together stay, couples who take on gods and killer aliens between date nights have more going for them than a typical Friday night fling. But threats like Doomsday, Brainiac, and Cyborg Superman are not the kind of threats that can accommodate a date night. As a result, there's a noticeable lack of balance for Superman and Wonder Woman as a couple. However, the struggle for them as individuals is still plenty compelling.
When Superman became infected with Doomsday, he became one of those problems that can't be worked out by cuddling with Wonder Woman over a candle-lit dinner at an overpriced restaurant. The struggle to control the urge to bring death to anything more complex than a bed of dead algae has been the driving force behind Superman: Doomed. It's a struggle that Superman has to fight on his own because most of it takes place within his own psyche. The persona of Doomsday and the persona of Clark Kent are constantly at odds, wrestling for control. It's like an arm-wrestling match with one of the contestants being on steroids.
This is a struggle that Wonder Woman can do little to effect. She was already able to do her part by helping Superman get off the planet and away from innocent people. But when Superman is forced to return to Earth to deal with an invasion by Brainiac and Cyborg Superman, Wonder Woman has to do even more. However, her struggle isn't as personal because the Justice League and the rest of Earth's heroes get involved as well. Even a power couple needs reinforcements at time. Love alone is not a viable defense against alien drones.
The scale of this battle is well-developed and more than appropriate in the context of the story. It would have been easy to shrug it off and assume that the heroes of the DC Universe are so used to fighting off alien invasions that it's not a story worth telling. For a story built around personal struggles, it provides a greater perspective that is easily lost in big crossover stories in the same way a chirping bird is lost at a rock concert. However, this also has the effect of limiting the collective struggle between Superman and Wonder Woman that gave so much weight to the drama in this battle.
In the midst of this global battle that involves some of DC's biggest heroes, Wonder Woman has to confront Superman again. And once again, she has to fight him while he struggles to regain control of himself. But it's a struggle that becomes secondary in wake of the many other ongoing conflicts involving Brainiac and Cyborg Superman. That's not to say the priorities aren't in order. A global invasion and a psychopathic alien intelligence definitely takes priority over personal struggles. Because of that, Wonder Woman's struggle to help her lover has a limited impact in the overall struggle. It's more a salad than a main course.
That's not to say there aren't some emotional moments in this struggle. Wonder Woman's presence definitely affects Superman's inner struggle against Doomsday. And Wonder Woman is certainly affected when she comes close to slaying Doomsday. However, these emotional moments lack significant depth. There's never that heart-wrenching, Old Yeller level struggle. The way Superman is able to assert control over Doomsday just seems too easy and too smooth. It's pretty jarring from earlier struggles in this story, many of which involved a more intimate struggle with Wonder Woman. This didn't really come off as one of those struggles that they would tell and re-tell their grandkids one day. It felt like one of those more tedious steps in a much larger conflict.
That overall conflict is still unresolved. Superman is still infected by Doomsday and the invasion by Brainiac is not over. Superman/Wonder Woman Annual #1 succeeded in expanding the scope and scale of this conflict, but did little to expand upon the personal drama. It had the feel of a Superman comic more than a Superman/Wonder Woman comic. There was plenty of room for melodramatic substance, but that room was taken up by theatrical style. Overall, it helped move the Superman: Doomed narrative forward in a meaningful way, but with less emotional weight than previous entries. This is still a conflict that's going to require more than a few date nights and flower bouquets to work through, but it's not going to require extensive couple's therapy just yet.
Final Score: 7 out of 10