I have to disagree strongly with other commenters. My long-term partner and I also applied together and fortunately got into the same school, but we were prepared to potentially be apart during medical school. Looking back, that would have been the biggest mistake of my life. Medical school gets really, really hard and I can’t imagine how tough it would have been alone.
The schools really aren’t that different, and I can say pretty confidently you’ll come to regret your decision if you choose Western from an emotional well-being perspective. If you are interested in EM or primary care, you will be just fine in Kansas. As for the allergies, can you see a specialist? They have options like allergy shots (I’ve personally done this and it helped a lot).
Please, please do not voluntarily choose to be away from your partner if this is a relationship you value. Reasons for choosing Western over Kansas seem minimal to me, and I think your mental health will suffer horribly being away from your only support. Support is huge in med school!