Indeed, Lucene 4.1+ may be a bit slower for indices that comptelely fit in your file-system cache. On the other hand, you should see better performance with indices which are larger than the amount of physical memory of your machine. Your reading benchmark only measures IndexReader.get(int) which should only be used to display summary results (that is, only called 10 or 20 times per displayed page). Most of time, the bottleneck is rather searching which can be made more efficient on small indices by switching to an in-memory postings format.
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