My tuppence worth...
We could do a lot to separate the flows at Leeds by building a short chord to take the trains from Bradford Interchange to where the four tracks from Armley currently join (roughly speaking: Copley Hill to Whitehall Road. This would take roughly 400 metres of viaduct and not require any land take (except from possibly either Leeds Council or the Highways Agency).
I would then extend the throat of Leeds Station to the North and add two (or perhaps even 4) for the displaced Harrogate and Shipley lines. This would take approximately 500 metres of viaduct. The new lines would then use some of the existing platforms and/or have new ones where the car park is currently situated.
I would also add another line to this throat to separate the Woodlesford line services from the Huddersfield ones.
(I know this might interfere with my idea for having the HS2 terminus there, but you could have low-level for Harrogate and Shipley lines and high-level for HS2.)
So the existing lines A to F into Leeds station would become E to L (excluding I), and you would have
A-B (New) Harrogate Line into new platform
C-D (New) Shipley Line into new platforms and existing platforms 1 to 2
E-F (formerly A-B) Caldervale Line into existing platforms 3 to 4
G-H (formerly C-D) Wakefield Line into existing platforms 5 (local) 6,8,9 (Long distance) and 10 (local)
J-K (formerly E-F) Huddersfield Line services onto existing platforms
L (New) Woodlesford Line onto existing platform 17.
This would mean that the Caldervale services would be cut off from the Neville Hill line. I think that this is worth it in this instance, as it would create masses of capacity. There may still be a clash for the Cross Country services, but that could hopefully be lived with.
(I think I've said the above in a previous post, but I can't find it.)
As for passenger capacity, I'm not aware of a huge problem on the concourse or the platforms (someone please tell me if I'm wrong). The proposed southern entrance would help a lot in that regard, though. I think it would take approximately 20% of passengers, who would also benefit from a shorter walk. If there are problems at the ticket barriers, then that area can be opened up by getting rid of the shop there (I think it's a sandwich shop), and providing more barriers.
However, having said all that, personally I don't think that the biggest problem for rail in Leeds is Leeds Station. It has already been mentioned that the biggest constraint for travel is the length of the trains. Once we have got rid of the 1,2 and 3 coach trains and replaced them with 6 coach trains and we still have a problem, then it will be time to get the chequebook out. Rolling stock is what we need! (And I say this as a civil engineer, who would probably benefit more from bridge/station works!)