As with everyone else, the reason I've heard is that ARROW is antiquated. When Amtrak replaces its reservations system, the new one may be able to handle the complicated problem of selling MBTA, Metro-North, LIRR, NYC Subway, NJT, SEPTA, MARC, Baltimore MetroRail, WMATA, VRE, SunRail, Tampa TECO, TriRail, Miami Metro, Metra, CTA, South Shore Line, Twin Cities Metro, Denver RTD, UTA Trax & Frontrunner, DART, St Louis Metrolink, TRE, NM RailRunner, Tucson SunLink, Sound Transit Sounder & Link, TriMet, Sacramento LRT, BART, SF Muni, VTA, LA Metro, LA Metrolink, Coaster, Sprinter, and San Diego Trolley tickets.
Or at least more of them than it currently handles.