The intelligence files leaked by the whistleblower Edward Snowden have highlighted two major issues that are specific to Britain. Neither have been welcomed by the government or our security agencies, and most of the political classes are trying to ignore them too. The first involves tactics.

Thanks to Snowden, we have found out about techniques that have given GCHQ the capability to suck up vast amounts of people's personal data from the cables that carry the internet in and out of the country.

The programme, called Tempora, is unquestionably ingenious, but it is underpinned by laws that are outdated and poorly worded.

Even the most sympathetic of scrutinising bodies – the parliamentary intelligence and security committee (ISC) – has put a question mark over this legislative framework.

The second issue involves British strategic thinking. The files seen by the Guardian are explicit about the importance of the UK's relationship with the US, and the desire for GCHQ to be as tightly bound as possible to its US counterpart, the National Security Agency. They will doubtless be welcomed by anyone who believes that the need for a "special relationship" with Washington – which has underpinned UK foreign policy since the second world war – is pre-eminent.

But in the light of these latest revelations, it is also right to assess the price we are paying for this relationship, and the compromises that come with it.

Without Snowden, we would not have known that the NSA pays GCHQ tens of millions of pounds a year.

These are the payments we actually know about – there may be others, because so many of our intelligence projects and programmes are historic and interlinked.

Yet none of the bodies that have notional responsibility for overseeing the money flowing into and out of GCHQ – the National Audit Office (NAO), the public accounts committee, the ISC – have ever mentioned these sums.

The NAO and the public accounts committee almost certainly didn't know about them. It is worth dwelling on this. The US government is paying money to support Britain's most important intelligence-gathering service. Would this be regarded as normal, or acceptable, in any other institution, such as the police or the military, both of whom work closely with the US?

And what does the US expect to get from this investment? Quite a bit, seems to be the answer. The influence the NSA has over GCHQ seems considerable. Whether this is down to the money, or the pressure a senior partner in a relationship can bring to bear, is not entirely clear.

Common sense suggests it's a mixture of the two. What is clear is this: the Snowden files are littered with remarks from GCHQ senior and middle managers worrying about the NSA "ask" and whether the British agency is doing enough to meet it.

One budget report states GCHQ will spend money according to NSA and UK government requirements – in that order. Does GCHQ feel compromised by this? If it does, it seems the imperative of keeping close to the Americans is overriding. That appears to be the view of the Cabinet Office too.

Asked about the NSA payments, the American demands and the concerns that the UK might be vulnerable to being pushed about, the Cabinet Office said: "In a 60-year close alliance it is entirely unsurprising that there are joint projects in which resources and expertise are pooled, but the benefits flow in both directions."

It may be entirely unsurprising in Whitehall that our subservience has been institutionalised in this way, but everyone else is entitled to ask whether that makes it healthy or right.

People are also entitled to ponder whether the price of keeping the Americans so close might involve undertaking some of their "dirty work" – developing intelligence-gathering techniques that are beyond the US legislative and judicial framework, but can be accommodated within ours.

Critics of the ISC argue it is simply too under-resourced and uncritical to give plausible answers to such questions; and the pronouncements of ministers who sign hundreds of warrants every year are hardly reassuring.

It would be naive to think that the US and the UK could work – or would want to work – in isolation of each other when its government-class shares many of the same perspectives on the world.

There are many advantages to sharing intelligence. But sovereignty and independence are important too. The NSA and GCHQ seem deeply enmeshed and interlinked, but the line between the agencies needs to be drawn more clearly.