I'm not sure if I'll tell you anything new but here goes.

On the iSeries side, have you created a view and are using that view in 
your application?
On the iSeries side, in the CREATE FUNCTION statement, what are you 
returning, a table?

If you answered YES to both of the above, basically, the iSeries is 
pulling the entire table from Oracle 
and then implementing the view over that table. When the program is 
running, do a WRKJOB and take option 14 
to look at the open database files. You'll see a table with a name like 
QUERY000x that shows the count. 
Once the entire table gets to the iSeries everything seems to run quickly. 
That's been my experience.

In order to speed things up I sometimes hard code the WHERE clause in the 
Java program.
On large tables I've found this speeds things up considerably but it's 
still slow, too slow for use in interactive or web based applications. 

Let us know if support comes up with something.

Best of luck

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