Regarding the road infrastructure, they need to remove the onramp from Columbia into 93 south and exit from 93 north to Columbia. Traffic coming on 93 north can get off at Morrissey Blvd. Create a new onramp at Freeport Street to 93 south (remove the existing small onramp) and widen 93 south by 1 full travel lane for a half mile here so people can safely merge onto 93 south. For a portion of this .50 widening, there's already an existing emergency turnout area and it abuts parking lots. I would also widen 93 north by one full travel lane from the existing Freeport street exit to Morrissey exit to allow people to safely exit 93.
This, coupled with a redesign of the rotary, would go a long way to improving the pedestrian and bike setup around JFK/UMass.