I've ridden a lot in Boston, Chicago, Santiago de Chile, Oslo, Salt Lake City. In general, on that list, the two easiest for the passenger are Oslo and Salt Lake City, where the same agency runs buses, trolleys, subways in Oslo, and trains, and has them in the same fare structure with the same fare system. The hardest for the rider is Chicago, where Metra and the L are totally separate, use totally different fare structures and payment systems, and, due to unfortunate inherited designs, don't even connect with each other at the same stations. In Boston, the T is a bit of both: Commuter Rail connects well to the subway, and there are passes that cover both, but one can't get a one-way ticket that covers both systems.
Not every place needs to do what Oslo does, and have all modes of transportation cost the same within a given zone or across a given set of zones. I can see reasons to charge extra for express services, whether that's commuter rail instead of subway, express buses, or something else. UTA in Salt Lake does that smoothly, using one payment system that can sell a ticket from any station to any other station, priced according to distance and modes needed. But splitting up the T's partially unified system would make things more complicated. Apart from potentially breaking up the website, trip planner, holiday scheduling, and other customer info, it would create two separate entities fighting for funding, possibly leading to a Chicagoland result -- way more money for commuter rail than for subway and bus. And that outcome wouldn't be good for anyone except suburbanites who work close to a CR station, esp if the two entities no longer gave a good deal on combined CR-subway passes.
Boston CR is perhaps more different from subway than Chicago Metra is (especially the Metra Electric district). It is certainly more different that Oslo train service, esp. on the busy main line, is from subway service -- headways can be similar. Possibly Boston CR should change to be more transit-like: more frequent, therefore possibly electric, more automated fare collection. But that doesn't really matter; whatever happens, Boston CR and transit should be part of the same system.
I am not saying the same entity has to physically operate the the trains, buses, trolleys, subway trains, commuter boats, but I am saying that the same entity should set the fares, sell the tickets, and probably determine the levels of service, and especially tell passengers how to find their way. It's just going to be an easier trip that way.
Anyone who wants a counter-example could consider Tokyo, where two different subway companies run more or less identical services, JR East runs above-ground service on the same headways and in the same basic style of equipment as the subway companies, and a few "private railways" run suburban service from pretty far out of town into downtown via trackage rights on regular subway lines. But there there are similar fares for similar service, a single plastic card to pay all the fares, and a possibility of passes that cover either one subway company, both, or subway and train, IIRC. More than three entities, almost seamless travel, except for extra turnstiles here and there. But I doubt separating the CR from the rest of the T would lead to a situation anything like the one in Tokyo.