First, a player can transfer into a D2 school and generally receive the one-time transfer exception, assuming his academic progress, etc is OK. The newly restrictive rule applies only to transfers into a D1 school.
So, assume a D3, D2, D1, or NAIA player has competed during his freshman year of 2009, transfers to a D1 in the fall of 20009, and doesn't compete (by rule) during the spring of 2010. He then has 3 more seasons (2011,2012,2013) of competition remaining.
For D1 schools, there are two aspects of eligibility that may come into play here. The first is that a player has 5 calendar years after first enrolling full time at any collegiate institution in which to compete in NCAA sports. Secondly, absent a hardship waiver, a player can only participate in 4 seasons of competition. However, fulfilling a residence requirement after a transfer doesn't consume a season of competition.
In the example above, the player, even with the one year of sitting out can compete for 4 seasons while still inside the 5 year window. There are other scenarios (for example, player redshirted his freshman year, i.e. voluntarily didn't compete) in which the 5 calendar window will expire before he is able to get in 4 seasons of competition. Also, players who didn't qualify academically when entering college have to sit out a season, and they generally (but not always) lose a season.
So, in plain English, in answer to your question, the player will have 3 seasons of eligibility starting in 2011.
