Oh sure, I agree that problem justifies some investment. But I don't think this was it. The Leeds-Clayton line that was reported to be in the plans, but turned out in the end not to be, would have provided a fast route out of Leeds, missing all the other nearby major population centres that need better services, before dumping trains only half-way to Sheffield for them to complete their journey on a slow and (as I understand it) already-at-capacity line. I can't believe that that's the best way to provide a Leeds-Sheffield commuter service. It would also have made Wakefield lose out heavily since fast trains between Leeds and Sheffield using the new line would no longer be able to call there. Note also that a straight line from Leeds to Sheffield passes through both Wakefield and Barnsley - the latter arguably in severe need of better rail services, but neither would be served by the line. Is there really a big enough market to justify a Leeds-Rotherham-Meadowhall-Sheffield service that misses out every other intermediate population centre?
Also consider that, as far as I can make out, for almost every new line that is being proposed as part of the plans, it's very easy to see how each line would easily support - say - a reasonably full train every 10 minutes or so running on it. That's a good use of money to build new lines. But this Leeds spur, lacking any long distance services, would probably justify 2, maybe at a pinch 3, trains an hour. That doesn't seem such a good use of money when the Government does need to watch how much it spends on the whole thing, and money spent on one improvement is money that's not available for another improvement. That's why I think it's a good thing that it's not in the plans, even while acknowledging that something (else?) needs to be done for the Leeds-Sheffield corridor.