Where did my fennel go?
Fennel is a fairly delicate flavor.  I can see how caramelized onion and tomato would easily over power it.  The bulb actually provide the most delicate flavor of fennel.  If you want a more pronounced flavor, I would suggest fennel seed.  I would further suggest you toast them first.  They can then be used whole, or, if you want an even stronger flavor, grind the seeds.  You could also garnish with the frond, but still that is rather delicate compared to using seeds.