Pisa and Lucca are the very northern part of Tuscany and are interesting to visit. If you want to explore the area I would land in Pisa, make the easy transfer to Lucca and spent two or three nights letting the jet lag wear off walking the wall and making the easy 30 minute train trip to Pisa if you want to see the Leaning Tower etc.
September is usually the end of the hot weather in the region area so depending on when you're there it may still be hot or starting to cool off a bit. There will multiple musical events - both free and ticketed - across Lucca every night in September so watch the notices around town and attend anything that interests you. Lucca has way too many good restaurants for a town of the size inside the city walls (9K population) so you'll have not problem eating well.
You are multiple combinations of train>train or train>bus to get to Siena from Lucca and not all go through Florence so check your options. Siena is worth at least a whole day for itself and is a good spot for arranging tours to nearby towns if you don't want to drive yourself. A spritz in Piazza del Campo as the sun sets over the square is one of the great Italian moments IMHO.
Have a great trip,
=Tod
