MOM definitely started out as a political supportive sound bite. It came at a time when NJ was doing amazing financially in the 80's and 90's. NJT was a model public transportation system for the country and even the world. That was when rail transit, particularly commuter rail, was on a comeback from decades of decline.
Whoever would get MOM rolling, which would bring back a massive amount of rail infrastructure to NJT, which would cause exploding development and growth (which means more tax $$$), would have quite the political prize for it. As a result, there was never a clear goal, and in all plans, the towns and NIMBY's all got upset that they would be getting shafted with each changing route.
Since then NJ has had a lot of financial issues, with NJT being one of the biggest ones.
That being said, MOM would need to be two lines under one system, and have multiple phases. The two lines would have to be a disjunction at Farmingdale, one going to Red Bank and the other to Jamesburg. The NIMBY's regarding both lines would equally get shafted (in their minds) so they would probably shut up if all towns along the SOUS/FIT had NJT come in.
Farmingdale-Red Bank would obviously the faster option for those further south, but Farmingdale-Jamesburg would serve towns out West, and give access to New Brunswick and Trenton (which would by default give access to Philadelphia). This would probably make MOM very successful if there were a variety of destination options with varying degrees of commute time. Sadly, the most optimal MOM plan, Farmingdale-Freehold-Matawan, is all but impossible, and the other options are too long/miss too many potential customers on their own.
MOM obviously can't *fully* happen unless there's new tunnels under the Hudson, but at the same time, the transit options down in Central and South Jersey are too dismal to be ignored or solved with more busses. If we wait for the Tunnels to be built, we won't get a single train on any of these routes until 2040 at best. That is just unacceptable, and who knows what could happen to the FIT or SOUS between now and then; it could go the way of the Freehold-Matawan route. That route, while abandoned, still had tracks in place on much of it, when they first started talking about MOM. Now the whole thing is a rail trail with much development encroaching on it, so that's a gauge of how fast things can change.
MOM should happen sooner rather than later. Even if it's a dinky shuttle service that gets people to either Red Bank or Jamesburg, it would reduce some congestion and definitely fill up some NJT trains on these routes.
Phase one would have to be as you said; some sort of shuttle. Ideally, it would either be light rail or single level DMUs. NJT could probably recycle a lot of Old Comet cars to do this. In addition, the terminus of MOM shouldn't be Lakehurst; there's really no purpose of servicing down there unless it follows the TRIT to the Toms River Park and Ride. If they are that concerned about money, just serve the biggest population centers first (Lakewood, Howell, Freehold, etc).
Phase two should be converting the line to dedicated single seat service to NYC. This obviously couldn't happen until the Gateway Tunnels would be finished. No more shuttles, make longer trains with the two leveled cars.
Phase three should be going south down to Lakehurst, through to Toms River. Serving Toms River, as someone said before, would be pointless unless it was a straight shot to NYC that was fast (IMO, the dedicated MOM trains from Phase 2 to NYC shouldn't stop at any non-major stops once they got onto the Coastline or NEC) or had access to Philadelphia. You would also probably have to increase the FRA rating of the tracks along the line to make it faster.
Obviously, I'm not a railroader nor employed by NJT nor qualified to run a railroad, but that's just my two cents regarding MOM. I think it is *extremely* needed and even a crappy initial version of it would be preferable to nothing at all at this point. I'm in Lakewood sometimes, a lot of the folks there are go back and forth from NYC; with gas prices now, I am pretty sure they would use MOM if given the option.
Sorry for the long post, I've had a lot of thoughts/ideas regarding MOM from all the replies I've read over the last few days.