MPDG is more about a relationship dynamic than a set of character traits. Personally, I think it's problematic to act like quirky girls are always problematic.
Two things to consider: a) boyfriends/girlfriends compulsively construct their girlfriends (and sometimes boyfriends) as MPDGs, and b) girls (and sometimes boys) construct themselves as MPDGs for the (supposed) benefit of their partners, people they want to date, and just regular friends (although hopefully not the closest ones because that's fucking unhealthy and irritating).
I'm a naturally kinda weird person who's pretty much over the phase of performing my own weirdness that I felt like I had to do to get people to like me in high school. I didn't start dating *until* I was pretty much over that phase, and I've still found myself struggling to break down the MPDG perception in pretty much every romantic relationship I've had, regardless of my partner's gender and how boring I felt like I was being. Conclusion: people want to be dating a MPDG. It makes them feel special. It makes the supposed MPDG feel like an object. An adored and fawned over object, but an object. It's hard to sustain any enjoyment of a relationship where only one of you feels like a person. Any self-respecting MPDG will tell their partner to cut that shit the fuck out at some point. If the relationship is worth keeping and the partner is willing to work on it, you develop a code. With my current boyfriend, he's allowed to talk about me like I'm a work of art until I say 'I've reached my quota.' Then he better start engaging me in some legit conversation like with a regular person (a kinda weird regular person with a brain full of hippy-instilled values and some mental health issues, but a regular person nonetheless). So far, it works. (And for what it's worth, we use John Green references to talk about stuff like this, and that works too.)
missesdash's advice to write some stuff from the MPDG's perspective is good. I would add that you should write some scenes of her where she's not interacting or even thinking about her love interest or anybody else she might be inclined to play up (or down) her MPDG-ness with. What's she like alone in her room, or eating dinner with her family? (Family's good. It's hard to play the MPDG card with family.) Watching movies in sweatpants with her best friend? Or even doing some MPDG-ish thing, like stargazing from a stranger's roof, or whatever she's into -- but in a situation where she definitely isn't doing it to impress anyone, just for the enjoyment of the activity itself. Write as many of these scenarios as you can come up with. The more aspects of her that have nothing to do with him that you know about, the better.
Now. How can you let the love interest in on that version of her? Because if you can't, that relationship is going nowhere.