Have postgis datastore redo the query plan at each request even with prepared 
statements
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                 Key: GEOT-2981
                 URL: http://jira.codehaus.org/browse/GEOT-2981
             Project: GeoTools
          Issue Type: Improvement
    Affects Versions: 2.6.2
            Reporter: Andrea Aime
            Assignee: Andrea Aime
             Fix For: 2.6.3


Testing shows that using prepared statements over GIS data does not give 
significant speedups, and in the case of some queries (bboxes as big as the 
data area) introduces a visible slowdown instead. Yet prepared statements are 
safer (no sql injection attack) and make dealing with dates much easier.

This thread talks about a parameter that, apparently, can be used to get the 
best of both worlds:
http://archives.postgresql.org/pgsql-jdbc/2009-05/msg00002.php

Give it a whirl

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