NJT will invest in Hoboken. They have no choice. Trains will terminate in Hoboken for decades to come and in all likelihood their number will increase somewhat. In spite of all the talk about Gateway, the only thing from Gateway that has reasonable shot of being completed in the next 5 years is the new Portal Bridge. For the two new tunnels you are looking at 10 years plus until opening. For Penn South it is basically never. Without Penn South no new trains will go to Penn during rush hour. While you might have been hearing that the tunnels are the choke point, there is not extra space in the existing Penn Station for new trains either.
I am quite disappointed that they separated the project into two phases. That will add at least an year, but in all likelihood two plus years to the whole project. They are receiving bids on extending the Jersey City sewer and filling the canal until July. One can only hope that the selection will be finished by October. Then it is an extra month for the board to vote on awarding the contract. More paperworks follows (permits, etc.), so by the time the equipment is on site it will be the first quarter of 2020. An year in construction follows. Once it is done they will start the process for the second phase: the elevated platforms, the new bridges over the streets and such. Expect another 3-4 years, so maybe in 2025 Hoboken will gain an additional tracks.
If I have to guess the separation in phases is because NJT does not have the money for the full project. The FTA money is probably enough to only fill the canal, not to build the tracks and the rest of the infrastructure. Completion of phase 1 will be a win though not only for NJT as it will reduce the chance of future flooding of the yard, but also for Hoboken as substantial amount of the flooding in the city came through the canal.