If your gods are patron gods, they are naturally going to favor certain things / places / people. The gods might also require or demand certain things of its worshipers. And certain gods might not be worshiped equally anyway. Some gods might only get offerings when you need something, or as part of rituals like weddings or before going on a difficult journey.

But you could also make the gods have disagreements and factions. Groups of gods that hate each other that form splinter pantheons. Gods that patron certain cities.
There could even be a disagreement about something major in the past - like two different gods both claiming they brought fire to humans.
Or a god that is going to one day destroy the universe and other gods disagreeing over if its a bad or good thing (or something that's even going to happen.)

I think some of the issues you're having are just part of what comes with making a world where the gods are real.