I do keep reading in various places 'let's improve the current network' as one objection to HS2. Well most people support improving the current network and that is being done. The trouble is most of the schemes you have mentioned above are vanity schemes at the back end of beyond, where there no real demand. The Ripon line is marginal, the Woodhead line has a case once capacity runs out on the current transpennine lines. The S&DJR has a cat in hells chance, even the comparable road network is rubbish. As for the highlands, it's very marginal whether we keep the current lines open.
Okay, what could you do with the ECML, WCML, MML?
Speed wise:
On the ECML there is a case to raise some speeds to 140mph in limited areas, which wouldn't actually save all that much time, and indeed reduce capacity.
The WCML is going pretty much as fast as it's likely to do with titling trains and it's current Victorian alignment.
The MML could be marginally improved in some areas, like the GWML. But again, with the mixed traffic nature of all these lines you are trading speed off for marginal capacity.
Capacity:
Can be improved, and is being improved by grade separation which is a limiting factor. For example Hitchin flyover, Reading and Doncaster. No doubt further grade separation will go in at Didcot and other areas. Again the chief limiting factor is the mix of traffic.
Other improvements:
MML and indeed the GWML could be electrified, which will help. The GWML and MML are currently being resignalled in some areas to improve reliability and increase capacity, the ECML will get ERTMS in the 2020s.
Why build a new HSR?
The chief reason to build it, and indeed this is pointed out in the DFTs latest business plan, is to shrink the N-S divide
http://www.dft.gov.uk/about/publications/business/plan2011-15/ and provide alternatives to the car and plane. We have a huge social and economic imbalance in this country, caused by de-industrialisation of the north. Prosperity is directly related to the time it takes to ride a train from London.
No other form of transport is going to realistically shrink this, especially south of Newcastle. You can build more motorways, but those would take up even more land and increase CO2. The problem is however, that traffic has to go somewhere, and it's better reaching city centres by rail rather than clogging them up with new road demand. Air can't even compete with the classic network south of Leeds. But BAA actually support HSR, because it's a far better way to access the airports than any other method.
Next, railways work best (and roads for that matter) when you have similar speeds and stopping patterns. HS2 gets the fast traffic on a separate line, leaving more space for commuters and freight. So, again it's not true that it's improving one thing at the expense of another.
I do sympathise with people that find they have a railway on their doorstep, but careful engineering and routing will ensure any disturbance is kept to a minimum. Certainly you can hide a lot of it away in tunnels and behind barriers, and it would take up less land and create less noise than a road. Nobody really notices HS1 in Kent.
In the end though, you could say this about anything: People don't want nuclear power plants, windfarms, airports, roads, large industrial areas on their doorstep either. But if you want to keep your modern mobility and standards of living, it is a compromise.
Finally on costs, it's about the same as free pensioner bus travel. It's 1/600th of the national expenditure for 15-20 years while it's being built, which will have external benefits once it's complete, greater ones that branch line repenings, improving bus services, and most road improvements.