Based on a 2010 paper by Anders Aaslund entitled Why Doesn’t Russia Join the WTO?, the main reasons were political and internal to Russia.
He unfortunately doesn't provide a summary anywhere in his paper, but from a cursory read:
- Officials were slow to decide it was important from the outset.
- (At least) 4 internal interest groups were lobbying against it.
- Putin eventually tried to push this forward, but his interest later waned.
They nearly gained accession in 2006, but there were still three obstacles then:
- The first was Russia’s poor relations with Georgia, already a WTO member. They basically were on their way to fighting a war around then. (This was the last obstacle, too.)
- The next was the U.S. Jackson-Vanik amendment, which was attached to the U.S. Trade Act of 1974, and appears to require Russia to allow jews to emigrate as a pre-condition for the US to open its markets.
- The last was that the EU, specifically Finland and Sweden, did not accept that Russia has decided to impose prohibitive export tariffs on lumber, which have been hiked gradually.
And in 2009, Putin convinced Belarus and Kazakhstan to join Russia in a Customs Union, which added an additional hurdle.
The whole process eventually took 18 years.