I'll address your questions by number.
1.) Yes, I am aware that Marylebone has only 6 platforms but this could be alleviated by extending the Tube to Aylesbury and upgrading the Princes Risborough-Aylesbury branch line to main line standard so that services that terminate at High Wycombe and Gerrards Cross are extended to Aylesbury Vale Parkway(fast between High Wycombe and Aylesbury), replacing the London Marylebone to Aylesbury directs and all Chiltern Railway Aylesbury line services.
This , I assume would also free up capacity on the Met for more semi-fast/fast Aylesbury/Metroland to Central London services.
2.) No I was not aware,please tell me how this could be rectified, if it could at all.
3.) Well I propose the Aylesbury Line services above to be removed to reclaim some capacity. I realise now that the reopening of the full GCR is totally irrational but there is no reason why Birmingham services can't be extended to Merseyside via Smethwick Galton Bridge + the WCML and the GCR still could be reopened to Rugby to take some fast shorter distance services off the WCML into Paddington if the capacity is available after Crossrail comes as you've told me Marylebone doesn't have the capacity.
I understand now that HS2 is needed but couldn't they at least put it in tunnel from Euston to Aylesbury to avoid destroying natural habitats. Yes it would cost a bomb, but it is already (possibly £100 billion) and I assume that they could offset a lot of householder compensation this way. I still believe in a Birmingham to Manchester HS2 Phase Two with branches to Newcastle via Leeds(and Hull) and Liverpool.Sheffield could also do with the reopening of the Woodhead line so some faster trains can avoid the stoppers on the Hope Valley Line and allow Sheffield residents to access HS2 that way. Railfuture says the Woodhead Line reopening would allow 30 minutes Sheffield to Manchester trains. That would allow Sheffield-London journey times of 1.38, better than the current MML times and potentially after HS2 Phase One opens, conventional fast service from Sheffield to London via Nottingham on the WCML. This would mean no NPR and savings from that can fund the tunnelling from Euston to Aylesbury
Regarding these points:
1) So you are planning to fit 140mph expresses in via Amersham amongst the 60mph Metropolitan line services that you've now extended to Aylesbury? Or are you instead saying that you'll send the expresses up the joint route via High Wycombe and mix them with the various stopping and semi-fast services which already exist?
2) To add more platforms at Marylebone would most likely involve demolishing a load of council flats and also an office block. Of course it's possible, but is both expensive (it's prime real estate in central London), and also met with resistance from the locals who will lose their homes.
Each end of the tunnel sections through St Johns Wood appear at each end to be double bored, but infact they are not. They were perhaps going to be but the GC ran out of money by the time it had got to London. I don't know what is in the way now but it would be cheap and probably disruptive to the running line next door to bore them out now. One benefit of building an entirely new line is to use trackbed formations which are actually suitable for the purpose, instead of the "Crayonista" view of joining dots that at first glance appear to work, but don't when you have the full details.
3) As earlier mentioned, you have essentially said that you plan to mix 140mph expresses with 60mph Metropolitan line services or 75mph stopping Chiltern services (it'll be one or the other). This is clearly not going to mix very well without separating the trains with a new pair of running lines. And so we get to one of the main points about HS2, which is to build a dedicated set of lines for these expresses. And since you're building it at great expense, it costs relatively little extra to make it a 250mph alignment compared to 140mph, so that way it's actually high speed.
Natural habitats will be lost by HS2, but it's a trade off between cost and habitat. The damage done by a railway is considerably less than a motorway. If you push the cost up too much, it will kill off political will to build the most needed part of the project in the first place. Phase one already has significant amounts of tunnelling and green cuttings to reduce blight and environmental harm; removing out later phases in the North to appease the Chiltern locals for blight to their properties won't go down well, politically.
The Woodhead route could be re-opened, but a lot of the capacity problems on the Hope Valley line can be solved with more goods loops and longer trains, which is cheaper than re-opening Woodhead (and finding a new home for the national grid cables which are using the tunnels). Compare this with the southern WCML which already can support maximum length trains and has no practical room for 6 tracking in many places.