I think this is a great idea, with some qualifications such as:
-Each year you re-evaluate your list with some considerable input given by others. Be willing to drop/add if necessary, even though the goal is to re-read them again and again. That is, in a few years, when you have grown more in maturity and in the Lord, by His grace, you don't want to be stuck only with what fed you in years' past when you were more of a babe.
-You don't let those twelve consume your reading so that you get nothing else read. For example, if on average you read 20 books a year, then 12 is too much and you should consider just reading 3 or 4 several times over. If however, you read an average of 50-60 books a year, then maybe 12 is a good goal to start with.
-You don't limit your 12 to one particular time-period only, within one specific culture of thought. Don't get me wrong, I love the Puritans and think that at least 6 or more of those books should be from their time-period, but every generation of the church had their erroneous tendencies and so keeping the list a bit diverse would profit you well.
-Consider what books other great men of faith have done this with. I know Fred Malone reads 'The True Bounds of Christian Freedom' every year. Spurgeon used to read Pilgrims Progress and the Reformed Pastor every year (or more). etc. I think you could get some great insight into what books profited the great men of old when read time and again.
Hope that helps!