There is no "oh, he meant well, and look at him, he's so sad, that makes it okay". Megamind himself acknowledges that Roxanne is completely in the right. He starts with trying to defend himself, that looks are deceiving, that he isn't as bad as people always think he is. But when Roxanne counters with okay, let's not focus on looks, let's focus on what you did, and lists off his worst past deeds, Megamind has absolutely no defense and he knows it. People might have judged him harshly from nothing but his appearance but he still decided to do what he did and he's responsible for his own actions. (Another thing that I love that the film manages so well! Sympathy is deserved for such a situation but that doesn't mean his actions in response to it become suddenly okay.) But it doesn't stop there! Because Roxanne doesn't understand why Megamind committed his latest evil scheme (lying to her and tricking her into a relationship) and asks him point-blank why he did it and why he's so evil for hurting her like this. And then the film communicates so much just with the look Megamind gives her and Roxanne's reaction to it. Because Megamind doesn't say "My goal wasn't to hurt you, I genuinely like you but you would've never been with me/I could never be with you being like I am" but his expression says all of that without words and Roxanne's response, how she can't believe it, tells us that she understood it too. And her answer is at the same time utterly brutal but also just matter-of-factly true and honest: She asks if he really thought that she would ever be with him, making her disdain for him as a person (with the aforementioned past actions) clear but also sending the implication that his "plan" wasn't sustainable and would've crumbled sooner or later, as soon as she found out who he was she would've broken up with him no matter what. And the choice of Megamind's answer to her question being "No" is so perfect! (I've seen reactions to the film where people automatically answer with "Yes" because that's the expected trope and then being even more shocked when Megamind says "No" instead.) Because it tells us that Megamind knows that he was deluding himself with this whole situation, he knows he has no leg to stand on. And you can argue that it's just him being self-pitying in a "oh nobody can love me :(" way but with the context of the rest of the conversation it doesn't come across that way. Roxanne made very clear what the reason is why she would never be with him (his evil actions which his tricking her into a relationship is a part of) and Megamind could neither defend nor justify them. It's certainly him feeling bad for himself to a degree but mainly it's him acknowledging that she's completely justified in not being with him because her objections are (painfully) accurate.* Megamind has no argument to bring forth for why he deserves a chance actually (and I love that he doesn't even try anything like "I did all these nice things for you tho!" because that doesn't change anything about his other actions and Megamind knows that) or for why, at that point, he isn't exactly as bad as Roxanne says he is, because he is. There's no feeling that Roxanne "is a b****" for saying all this, she's harsh and justifiedly angry and Megamind feels bad about it - and she's right.

And another nuance that I see people frequently miss or disregard when discussing Megamind tricking Roxanne into a relationship: Roxanne likes Megamind's personality, she likes spending time with him outside of his evil schemes (where she knew him as Bernard). They both enjoy each other's company so much. That's why she cites his actions (including lying to her) for why she would never be with him. That doesn't at all justify Megamind's lies, which is why he needed to apologize and redeem himself for them, and the sympathy we have for his loneliness is a reason but not an excuse. He didn't initially mean to trick her into a full-on relationship but he could've stopped at any moment yet he didn't. However, I've seen discussions about this topic where people frequently miss that Megamind did not actively change his personality or act a certain way to make Roxanne like him. How he behaves as Bernard is how he really is. Sure, he changes his name and optics and hides that he (as Megamind) did all these evil things to the city, but his reactions to what Roxanne says and does, his likes and dislikes, even secrets he can admit without giving his identity away? Completely genuine. He lies but he's not being manipulative. First of all, because Megamind doesn't have enough experience in normal human interactions to even know what to do or say to make people like him. If he did, he would've done so with other people already. Second, the one thing he can arguably infer that Roxanne likes in others (on account of also believing that she was into and together with Metroman) he doesn't do. Megamind acts nothing like Metroman in his interactions with Roxanne. (And that's despite him giving Hal exactly that advice, become their hero, about the crush he admits to him he has. Megamind seems to be too busy being in love with her to actively try to woo Roxanne which is kinda adorable.) Third, he does nice things for her but he doesn't use them to make her like him more. As I mentioned above, Megamind doesn't bring them up when he argues his case to Roxanne. He makes a comment once about "Megamind maybe not being as evil as they thought" as Bernard when he brought the paintings back so maybe he tried to lead into that eventually, but the primary motivation we can see from him directly is just making Roxanne happy. He listens to her and recognizes when she's sad about the state of the city and fixes it, specifically the things she mentions to him, being happy when he sees her being happy. That doesn't make him a morally better person all of a sudden but it does mean that he's attentive to her wants and what she says rather than manipulating her.

As I said, that doesn't make Megamind's lies go away, which is part of what he needs to be redeemed for, but it does mean that their relationship has a pretty strong, and surprisingly genuine, foundation despite them. They certainly need some time past the end of the film to work through all of this and (c/w)shouldn't jump into a relationship right away, but given the context of the situation and Megamind's and Roxanne's behaviour throughout it I see no reason to believe theirs wouldn't be a healthy relationship once they get there.