There will definitely be large benefits to having a North Side RER-style service through- run on the Framingham/Worcester Line to the employment and entertainment centers around Back Bay and Yawkey, on its way to a short-turn at Riverside or Framingham.
The issue is, as I see it, that every northern line (Fitchburg, New Hampshire Main, Boston & Maine Western, and Boston & Maine Eastern) has both the capacity and the demand for some sort of inner RER-type service. Of the southern routes, only Framingham/Worcester and Fairmount have both the capacity and the demand to implement 15-18 minute headways.
Worcester can handle it with signal and passing track upgrades. Fairmount is already ready for RT-like service.
Old Colony can't handle high headways due to the pinch in Dorchester. Removing that pinch is a megaproject all its own. Old Colony won't get a portal into the Link until that's done. No one will budget for it.
The NEC will be handling both higher frequencies of Amtrak service as well as higher MBCR traffic - especially after the Link is built. Projected congestion on the NEC will already eventually box out the Needham Line by choking it to death, so there won't be any capacity on the NEC for an RER to Needham. Needham's getting choked to death by the NEC's growth and will eventually need to be replaced with a Green/Orange paired extension. That means there won't be any 'MUs running 18 minute headways on the NEC. The capacity isn't there now and won't be there in the future.
If routed along the Fairmount, the Franklin Line could probably handle high headway service to Norwood or Walpole.
The first southern Link portal to be built will be for the NEC, which will likely also include access for the Worcester Line. The northern portal will likely be able to include both the Lowell Line and the Eastern and Western Routes (Fitchburg won't get one). Problem is, the Worcester Line will only be able to handle one high headway RER (pick Lowell, Reading or Salem/Peabody). With the initial build there's no other option for routing 18 min headway 'MUs through the link. That leaves any 'MUs running on the remaining four northern lines to terminate on the surface at North Station.
The next priority should probably be electrification and portal construction for Fairmount and maybe some of Franklin. There won't be as much demand for an RER to the Fairmount since there's no employment centers along it. Commuters will take a Link-running train to South Station, but not many will stay on beyond that because the Fairmount runs through residential neighborhoods. That lack of demand, and the high costs of building the portal and electrifying the line will make this one a political battle, but it's still probably the easiest way to get another RER-type line through the link.
Old Colony will have to wait until the Dorchester mess is funded and fixed, and Needham is getting squeezed on its existing schedule, let alone at higher headways.
Realistically, as far as transformational RER-type service goes, the most to expect is two high-headway,through-running routes (something like Lowell - Riverside and Peabody - Walpole). That's it for RER.
Of course the Link also allows Amtrak to bomb north to Portland, Portsmouth or Manchester. It also allows the traditional commuter rail to beef up capacity and through-run on routes that make sense, which will be a big deal for commuters who can have their one seat ride to South Station or Back Bay from the north, or North Station from the south.
The high-headway EMU RT-lite service is not going to be a panacea though.