10-minute sketch of how you could make it work. Basically just expand the size of the rotary to give you enough room for a junction with the access road. Not exactly going to make the interchange better, but I can't imagine it would make it much worse. There aren't going to be too many people driving from the south (since Riverside is closer to the Pike), and hopefully those closer to downtown Waltham can use buses to get there, so I would hope that will limit the amount of traffic having to do the additional weave to get to the station.
The station should be an island platform so that terminating trains can use either track. There's probably enough room under the existing trail trestle to widen the tracks and add the platform, but it's not a majorly historically valuable bridge. Up and over at the southeast end, and a gated grade crossing for the handful of pedestrians walking from the Kendal Green area.
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