There are two things that could be causing the delay. First, your mySQL database might not be optimized well. Take the query that you're sending to the database and have the database analyze it with EXPLAIN. Like:

EXPLAIN SELECT * FROM tablename WHERE ...

If you have a massively large database and are selecting a relatively small number of coordinates to plot, it's possible that the delay might be here. Post the results here, and look into making an index.

The other possibility is that your graphics rendering is just taking too long. This can't really be helped, aside from lowering the number of displayed points (either by ranking each point's importance and only displaying important ones, or by zooming in the map) or getting a more efficient rendering module. You might also look into using CSS layers to display the points, rather than actually generating a graphic for each view. This method won't be quite as compatible, but should take significantly less processing time.