Just went for a ride which made me think the following (playing devil's advocate).
1) CONI has DNA and blood, and since they know the DNA is from Valverde, and it matches the blood, it is easy to prove it is Valverde's blood. What I wonder is, that after such a long time, the enriched blood (which indicates doping) is still 'enriched enough' to prove doping. Unless of course a non-natural product is found.
2) Another thing is, how eager is UCI to admit certain evidence that has been obtained, perhaps illegaly, or that is still under criminal investigation in Spain, and cannot/should not have been made 'public'. It might obstruct justice in Spain, since it could turn his blood into an inadmissible piece of evidence. As a result, it might underminde the porces against Valverde entirely.
3) How will the UCI, or even CONI prove the 'intention to use doping'. Basso squealed at the first sight of doping charges, and since he assumed he would be cut some slack for cooperating (a wrong assumption), he pleaded guilty. If he had denied all charges, no one, I think, would have been able to prove anything.
To illustrate, if you have a loaded gun at home, you can't be charged for 'intention to kill'. At most, if you have gun laws, you could be charged for possession, but certainly no intent to kill. Valverde's gun was loaded, but not even in his possession (clever construction, Fuentes was in possession of enriched blood, ie the loaded gun), so how could they charge Valverde with intent, if he stubornly denies all charges. He could say that 'he had entrusted Fuentes with his blood for analysis' and that 'Fuentes had enriched it without permission'.
That would mean UCI needs circumstantial evidence, ie phone conversations, bank transactions, statements to porve Valverde entrusted him with blood to enrich it for the purpose of using it as doping. That however, the UCI does not have since it is in Spain.
4) The downside of 3 is that Valverde can be taken out of competition, even without an UCI ban, since race organizers deny him entry. This would in effect lead to the end of his career.
5) If the UCI or race organizers ban him/exclude him entry, he could potentially take it to the European Commission of Human Rights and/or the European Court of Justice, either for a violation of fair trial (ECHR) or (slighter chance) a violation of EC competition laws, namely that he is denied to work, as far as cycling is an economic activity, based on 'unfair' procedures, and perhaps violating certain social protection clauses. (In another instance, the domestic dutch court ruled that Rasmussen was unfairly fired on the spot, and paid 650000 euros in damages)
The problem is that it would surely take longer then 2 years, in which case he would jeopardize his career. Valverde is unlikely to pursue this path...
It still leaves wondering that if Valverde denies all charges, how they can keep him out of competiton fairly...