Actually I think it is clear in 2.0 that Shinji does not pilot Eva for personal pleasure. He went back only to save Rei, so he pilots Eva for someone else, not for himself.
The only one who gets immediate gratification from rescuing Rei is Shinji. Rei even pleads Shinji to abandon her, but Shinji keeps going on because that is what he
wants. He is acting on his own desires, with little care for anything or anyone else. If you do something for someone else without considering their point of view, you really can't say that you're doing it for them.
I think this point stands regardless of how one views Shinji's actions in relation to Rei's seeming resignation. In fact, i wouldn't be surprised if in the future movies it would turn out that by keeping her alive as a human existence, Shinji damned Rei to much greater pains than mere death. She now entered the realm of fully realized humanity, and that is where true suffering dwells.
As for the "destruction of the world versus Shinji obtaining his goal" thing, from a thematic point of view, a good interpratation might be to view it as a conflict between the freedom of the individual and the constraints of reality. As Shinji gains ultimate freedom via the enabling power of the Eva, the world that put restrictions on him is slowly disintegrating. However, if the process would have run it's full course, and the world as we know it would have came to an end (let's just run with the idea that this would have happened, otherwise their wouldn't be much of a conflict going on), then even with Rei by his side, his existence would have lost all goal, all purpose, all meaning, only reaching the freedom of nothingness, essentially. IIRC, something very similar was touched upon in EoTV.
(... having performed his "survivor's duty" (Kaji) and overcoming all obstacles to his goal (Gendo).)
Those two are kind incompatible, at least in my view. I mean really, how do you reconcile "surviving pain and hardship can make you a more considerate, better person" with "be ruthless, you'll get the pony"? One may argue that elements of each leasson are present in Shinji's actions, but if we assume that, then we have to dilute the rather straightforward words of wisdom imparted on Shinji by Gendo and Kaji to a degree that their influence would turn minuscule, effectively like they said nothing at all.
For that matter, i think that the visual of the burnt water melon patch has nothing to do with anyone else other than Shinji. As symbol of growth destroyed, shown just after Shinji is spurred into action by seeing Rei getting devoured, who he has benn, well, nurturing, in a sense. Making her "grow".
For my two cents, i am of the opinion that Shinji ultimately sided with Gendo and only Gendo in his world damning antics. Not being able to deal with the pain of loss (like Kaji suggested he should be able to) is what (presumably) motivates both father and son to do the things they do.
And before anyone argues against it, yes, Shinji was damning the world, at least if we assume the line
I don't care about the world!
holds any meaning. If we suppose, like others have that "oh, he is only saying that, but it's not like he really thinks it", than the line, delivered in a highly dramatic situation with our attention directly called to it, simply fizzles, holding no valuable information. He could say anything instead, like, for example, "Yippee-ki-yay, motherfucker", and the scene would have the same meaning.
"Outside of a dog, a book is man's best friend. Inside of a dog, it is too dark to read."