(Spoilers to FFX-2)
When I first heard that Wakka and Lulu got married, I thought, "Say WHAT? What is Square THINKING?" It seemed like crack, it seemed cruel to Wakka, and it seemed disrespectful to Lulu. I came to the conclusion that it was a marriage of convenience for the game designers, getting Wakka and Lulu out of the way so that they wouldn't rush to Yuna's defense when the going got tough.
Crack because he was this nice ordinary guy, a heart-of-gold jock athelete, and she's a frickin' force of nature, with a deadly implacable streak. Neither one of them is on the same wavelength as the other. I certainly can understand their friendship; they have a lot of shared history and common ground. But that which makes them most themselves is not something the other will ever really relate to.
I could see playing them off against one another in fanfiction CRACK, the way one might put Selphie and Seifer, or, well, things like Aurikku where part of the game is that they're so different that it's bizarre. I know the whole opposites attract schtick. Wakka and Lulu are very, VERY opposite, and from what I've seen, those differences would put far too much strain on a relationship.
The second and biggest thing for me is that it seems mean to Wakka. He will always feel inferior around Lulu, and she will always be in a position of authority and power, even when she chooses to defer to him in the hopes of kicking him to make up his own mind. He loves her, sure. But he's scared of her. I don't see any sign in X-2 that he's grown a spine and is no longer in the "yes ma'am" mode he was in FFX (a phrase he did say to her).
I just don't think it's good for poor Wakka to be in a permanent partnership with Lulu. It's an unequal relationship where she holds the leash, unless she denies her own self-power and authority, and decides to let him be in charge. That's one of the big reasons why Auron/Lulu works so well -- neither one dominates the other.
I can see Wakka falling for her, but he would have done better with Rikku, where they'd fight and argue and get mad and neither one would feel eclipsed by the other.
Third is the hypocritical factor for Lulu. In FFX, she made it bluntly clear that they were incompatible on at least two occasions where Tidus hinted at something between them.
First response: "You don't want to finish that sentence."
Second response: "Getting along isn't enough. Not even close. You need to learn something about women."
"Okay, I won't forget."
"I won't forget either."
It's the second one that's really, really firm to me. Lulu knows herself. She is trying to instruct Tidus to pay a little closer attention to what people are like. She's trying to make a very important point (often lost on fanfic and other writers), that one can have male/female friendships that are not romantic.
Lulu says she's not going to forget. Then, according to X-2, she does.
I know people can lie to themselves, I know they can protest too much, I know they can have a change of heart -- but I hate it that Lulu turns out to be a total hypocrite, a fickle woman who doesn't know her own mind and heart. I'm tired of the "fickleness of women" plotline. I don't want her words to turn out to be a lie.
Also, honestly, I don't understand why she would've had a change of heart in how she feels about him. Getting over her frustration of Wakka to trust him as a friend, yes. Falling in love with him? No. Chappu was an ordinary guy (opposite, again) but he seemed to have a life, a spark in him, and I could see how that exact kind of magic and love and "come on, Lu, let's go!" might have helped her draw her out of herself. But Wakka's insecurities only draw out Lulu's frustrations. At best, she has to tolerate and gloss over his neurotic worries, his annoying habits, the things she finds foolish. I don't see anything in Wakka to ignite a romantic spark in a woman with Lulu's temperament.
Watching the two of them married, I see that Lulu has diminished herself and given up on a piece of herself in order not to hurt him. I see Wakka is still under her thumb, unable to be his own lovable self without a sense of shame. That's sad for both of them.
I can imagine writing the ship as an alternative to canon, playing with "what if the impossible happened and Lulu fell for Wakka the way he's fallen for her?" but as canon, it's disappointing. I have the hunch that most of the Wakka/Lulu shippers would not see it that way.
In my own writing, which is firmly FFX most of the time, I enjoy very much writing Wakka and Lulu as friends, and Wakka with a crush on her (poor Wakka). I will sometimes write on the assumption that maybe after the pilgrimage, Lulu gave in and let herself marry Wakka because he's there, because he's a friend, because she trusts him, because he at least understands her a little. But it's not an ideal match, and he'll never entirely live up to her expectations or fill the gap in her heart.
ETA: Wakka/Lulu fans, I am sorry that I got a little too forceful in stating my opinion in a few places here. There are definitely different ways of looking at all this. Please see some of the thoughtful replies below.