Quite a lot has changed on the network since then. EWR is not about rebuilding what was lost, but about building a suitable railway for future need.
Seems to me that "future need" has ended up going out the window, with various kinds of "it will enable..." things turning into "er well actually it won't", and minor things like additional curves at junctions getting stuck in the "not going to happen" bin, as the design gets pared back to something that is an exact match to the very specific proposed needs they have cooked up by anal extraction to look good in the latest report, and anything that might improve flexibility to allow for other uses arising in future or even being planned gets disallowed because it would cost a bit more and they've already wasted enough money fannying on with endless reports while the cost endlessly rises to have had it open already if they'd got on with it in the first place.
What it looks like we're getting is something that doesn't even get as far as restoring what was lost, meets only a very narrow specification for "future need" and no more than that, and is inflexible enough that it will never be able to meet any kind of need which differs too much from that - whether as a future possibility or even that is currently known to exist - without a disproportionate amount of grief building some small extra bit which would not have been a significant extra hassle if it had been done at the same time as the rest of it.
I find the lack of consideration for north-pointing connectivity particularly disappointing. It seems to have ended up with far too many junctions pointing the wrong way for a lot of otherwise possible freight traffic, without any chance of curves to fill in the missing direction, and the discussion in this thread about logical connectivity for passenger services getting the same treatment and nobody seems to care is most depressing. It's a long-standing deficiency of the railway network in this country (and the roads too, to a lesser extent) that it seems to assume that the only place anyone ever wants to go to is London, and you can safely ignore the idea of people wanting to go somewhere else. If you
do want to go to London, or to somewhere that's on the way to London, it's pretty straightforward. If you want to go crossways, or make a journey that turns away from London, it's a lot more difficult and a lot slower. It gets difficult even to argue that the non-London-based connectivity should be better, as "nobody bothers trying because it's too much of a pain" gets interpreted as "no demand", and any example of a particular journey for which such improved connectivity would be an advantage tends to get the response that the number of other people wanting to do that exact same journey isn't enough to justify making it easier, which may be true on its own but ignores all the hundreds of other possible journeys that a few people want to do which would share in the improvement.
That some currently awkward journeys are in fact comparably quick if you make a 200km detour into London and out again - which in some cases does actually seem to be true - does not mean that the situation is "fine" and doesn't need addressing. If a more direct route can take roughly the same time as one that goes 200km extra, it means the journey is far too slow either way and the direct route is rubbish. It doesn't make it less rubbish that a much longer route isn't more rubbish; it means they both are, and the situation does need addressing. Not to mention that operators who go in and out of London tend to hammer you much worse on fares than ones which don't.
I had always hoped that EWR would make a significant difference to this problem, and it is most disappointing to find it being described as concentrating only on east-west traffic within its own arc plus whatever bit it can pick up from people in the mostly rather small places that currently don't have a railway wanting to go to London, and actively declining to consider those who want to go the other way or to use it as part of a longer crossways journey. I agree with the various posters who say what a pain it is making crossways or crossways/northwards journeys by the means that currently exist: the journeys I've made that share in some of the routing have always been a grind and a bind, and if there's been a choice of routes both have been awful. I also concur that "change at Bletchley then at MK" and its relatives do suck.
I do admit that it's a difficult problem to deal with the suboptimal alignments at all the points it intersects north-south main lines, and I am thoroughly impressed with the current idea of going north-about Bedford, which I thought was too unlikely to bother thinking about (though not installing an east-to-north curve while they're digging all the rest up is a deficiency). It works much better than any of the ideas which stuck to going south-about would have (some of which were terrible), given the constraint of using the Marston Vale line. I guess that constraint was sort of inevitable, but it's going to be a long-standing problem having that stuck in the middle of it with so many stations, no loops, and all the level crossings which are impossible to remove, and it excludes any decent possibility of dealing with Milton Keynes having been built in the wrong place. Commuting between Bedford and MK will remain unfeasible. I would have preferred to see them revive the old Victorian idea of carrying on from Newport Pagnell to join the Northampton-Bedford line near Olney, then do the zig-zag through Bedford the opposite way and come out along the old Sandy route, which would add MK to the route in the same way they worked Bedford in and avoid the Marston Vale bottleneck.