You're way too optimistic about the EU's role in defence policy. You have 4 clusters of air forces in Europe : those that will always rely on US planes, the Typhoon consortium countries, France with its Rafale, and the Gripen countries.
Politically, getting all the EU countries to agree is a pure nightmare, never mind a defence programme worth tens of billions of euros and tens of thousands of high tech jobs.
One last thing : instead of thinking of how a Typhoon will look like in 2040, how about thinking of how our air forces will look like in 2015 with hardly any F35s in service and only the Typhoons remaining alongside ?
A shared, common security and foreign policy (GASP in Germany, Gemeinsame Außen- und Sicherheitspolitik) is one of the pillars of the EU founding. Especially in recent months the idea of a EU military came up again, and in 20 to 30 years time we might just be there already.
And I think you underestimate the power of the Eu parliament and what far-reaching consequences EU law and directives have. Politicians don't really like to tell their peons, but the EU is a sticky fly trap: There are no regulations that govern leaving it and while only restricted by respective national constitutions in application, EU law are immediately effective for the whole EU and directives have to be turned into laws by the nations themselves, but according to the instructions given in the EU legislative directive.
Now, most countries have their military and power over military and sovereignty and military sovereignty defined in their constitution, so there still is a hurdle to climb. Even though past efforts for a common EU constitution failed (France and the Netherlands voted against it), we are already farther ahead now than we've been 10 years ago: We signed a European Human and Civil Rights Charta this year, a founding stock to a future constitution. It's going slower than some perhaps expected or wished for, but it's happening.
And if Great Britain, France, Spain, Italy and Germany pull in one direction and reach a consensus on something, I'm willing to bet that they can drag everyone else along.
Tornado = GB, Italy, Germany
Typhoon = GB, Italy, Spain, Germany
Next one = GB, Italy, Spain, France, Germany?
Well, speculation of course, but I think Europe will turn into a kickass confederation.
Well, to come back to the Typhoon: A biofuel mid-life update would actually be something worth investigating I think. Less consumption, cheaper propellant and perhaps coming from a renewable source.