The first is that it seeks to tinker with a machine that is fundamentally flawed. Of course Sir James is correct that it is madness to herd high-calibre graduates back onto aeroplanes as soon as their degrees are finished. But the solution is not to grant an extra few thousand places to the chosen ones. We should not be deporting (or denying access to) anybody who wishes to work in the United Kingdom. Similarly, Capital Gains Tax that discourages investment should be relaxed, not just for those investing in high-tech, long-term projects, but for industry as a whole. Car manufacturers and steel works are as susceptible to the effects of Capital Gains Tax as inventors.
The second is that Sir James is falling into the trap of thinking that he knows specifically what the economy requires. However, Sir James is no more able to predict the specific needs of an economy than the Government or a guest blogger at a think tank. Sir James may be right that UK needs to invest more in innovation and welcome more numerate graduates, but he may equally be wrong. Recent events have demonstrated the danger of assuming that current trends will continue into the long term. The UK may in fact need infrastructure rather than innovation; or it may require linguists more than mathematicians. Rather than creating distortions in the market, the government would be better letting the market perform its discovery process.
As for incentivising (forgive me!) long-term investment, there is a very simple and non-distortionary means of doing this: raise interest rates. Interest rates represent the return on investment: if they are low, long-term investment carries little reward; if they are high, long term investment is very rewarding. Austrian economists would argue that these, too, should be set by the market, so that they correctly reflect the time-preference of society (do we want to consume what we have today or a larger amount in the future?).
It is understandable that Sir James would like to promote an innovative Britain. A man who invested £2,000 and created a company worth £500m could be forgiven for thinking that projects like his are the future. But the future is not yet written, and a 25,000,000 per cent return should be incentive enough for anyone.