How do you deal with this?

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I have a mixte and a regular step through also. Skirts with shorts or pants under them work perfectly on these. You can usually find a mixte on ebay or craigslist for very little. Check out this thread.
The current "modern" mixtes are pretty pricey (and by the way, those bikes by Trek are not considered mixtes). You can get a classic, however, and they are perfect commuters. Outfit it however you like. Baskets, moustache bars, etc. Once you look at that thread you will have to have one!