Amtrak, for their main locomotive fleet, needs something that can fit into Penn, as mentioned. But also, the MP36 is a fairly weak loco- 3600 hp. It also has limited range. None of these things matter on a commuter engine, but for Amtrak's needs, they are all deal breakers.
Lastly, the MP36 is highly compromised by its design which is intended to be built generically in relatively small numbers. Amtrak has specialized requirements, and also has a diesel fleet of some 250+ locomotives, as opposed to the individual commuter roads which have few locomotives.
Keep in mind that none of the three big commuter roads use the MP36- NJT, LIRR, Metro-North. NJT has some old F40s and Geeps, plus their 33 Alstom PL42s, which are European in design and unique to NJT, with the rest of them scheduled to be replaced by Bombardier ALP-45DP Electro-diesel dual modes. LIRR uses DE30s and DM30s, both EMD and of unique design to that road (and are admittedly junk). Metro-North uses Genesis locomotives, both P32ACDMs and P40s bought from Amtrak. They also have a few F units around. They technically own a few F40s and Geeps, but those are used by NJ Transit.
Amtrak, NJTransit, LIRR and Metro North have something in common- they are all huge. When they buy power, they can afford to amortize the cost of an engine best suited to their needs, even if its a clean sheet design.
Really, when you get down to it, the MP36's main advantage is its low price.