Being in a girl's route or not doesn't affect anything main story-wise.
However, you'll miss the harem scenes she may be on in the future.
For example, her, plus one or more characters.
Also, lose one route, you'll miss the all-or-nothing route, which will start soon. Also, unlike Gwen and some, certain characters' future arcs trigger within a certain harem/rival route, like Sky in the SkyXGwen back on the beach island.
All or nothing route will be the prominent route, 'cause harem. The main game ending will be taken from this too.