Uhh, yeah, they're so completely different I really don't understand this mentality of comparison at all ever. They are so different and non-exclusive to being liked, this way of thinking needs to die. I'll talk about them both a little bit.
As long as we don't include the ruinated reboots that JJ Abrams did/is doing of both franchises... I love them both! They both have a lot to them. I don't like all of the content for either of them, certainly.
Star Trek is more intellectual. It is social commentary, ethical quandary/moral dilemma, what-if encounters, and personal relationship dynamics within a world of exploration and discovery.
Star Wars is more philosophical. It is about positive and negative forces being a part of the world and the balance between them. It is about facing the darkness within ourselves, finding the ways to be good and exemplifying it into our ways of being despite the temptations of greed, power, control, blind loyalty to authorities, and ease of living that draw us. It's about the power of the choices you make and how those choices guide you into the life that you have. It's about overcoming your fears and controlling your anger and not letting it control you. It's about redemption and, regardless of how far we fall, how there is a path to the light if only we embrace it and work to quiet the evil within.