There are a lot of things about Hanji that he likes.
He likes the way her eyes dart around when someone calls her name, and how they sparkle when she smiles or gets excited. He likes how she can cross her second toe over her big one on her right foot (and only her right, but not for lack of trying). He likes when she pushes her goggles up on her forehead when she does her experiments. He likes the way her hair curls around her shoulders in the mornings. He likes the long, twisting, puckered burn scar that starts on her left hip and snakes up her side and briefly over her stomach almost reaching her armpit (she has dozens of scars of course, some even worse, but that one interested him the most because it definitely wasn't the kind of burn scar you got from a Titan, although he had yet worked up the courage to ask about it). He likes her snaggletooth, the little one on her lower jaw that's actually kind of funny because the rest of her teeth are perfect and straight, and he likes the way she doesn't seem to care. He especially likes the way she talks to him, like he isn't anything special. He'd kill for more people to treat him like that (although that might get the opposite of the desired effect).
These are little things, fairly insignificant in the grand scheme of her but important to him nonetheless.
It's times like this when he considers telling her these things, times when he pulls back to look at her and is suddenly struck by just how beautiful she is, but he knows that if he did she would laugh, tease him and call him a "big ol' softie," then maybe hug him. Not that that would really bother him, even if it made it past the confines of one of their rooms or her lab, but because it's just so silly, so domestic. Not fitting of a soldier at all.
So he just settles for kissing her again, and hopes it gets his point across well enough.
(at least, until there came a time when he didn't have to settle anymore, but that is neither here nor there)