I suspect there is some very high-level political gamesmanship going on here, and not just between the RAF and the RN. The UK/US mutual defence agreement is up for renewal, so Trident, Cruise and nuke cooperation is all being reassessed - and in the aftermath of 9-11 and in today's post Cold War world there are serious questions being asked in America about the future of NATO and the relationship with allies. Without US cooperation we have no Trident, and no Cruise. So it's either a freefall weapon or adapted Storm Shadow - requiring French cooperation?
A clear signal from the UK that we intend to remain a 'major power' will doubtless have some sort of input on US deliberations, and Blair's insistence on getting involved with the US in Iraq (despite US misgivings) was quite possibly a strategic ploy too.
http://www.acronym.org.uk/dd/dd76/76news04.htm
US-UK Nuclear Weapons Cooperation Up for Renewal
http://www.basicint.org/nuclear/NPT/2004pc/1958MDA.htm
1958 US-UK Mutual Defence Agreement
[edited for spilling]