There's a local chain called Austin's Pizza that is good. Their whole wheat crust is a free option. Their ingredients are generally very fresh. The pesto sauce they serve is not strong enough, but the bbq sauce from Stubb's BBQ makes a mean bbq chicken pizza.
Their wings never show up to my place still steaming hot. The wing sauce tastes homemade, though it uses too much butter. And you have to try their homemade "atomic ranch." There's nothing spicy about it, but the flavor is great.
And just the other day my roommate and I had a nice pizza from Texas Pizza, Pasta, and More, which might not deliver to your area (They're on Airport near where it stops at Lamar). They serve nice 18" Jumbo pizzas, and they're as cheap as a national chain.
The internet warned me about them, though. Some guy (I can't find the link) ordered something with seafood and then complained that it was imitation crab meat. So, ask about that before you order any seafood. And their wings weren't great.
2324 Guadalupe St, Austin, TX
Texas Pizza Pasta & More
6929 Airport Blvd # 158, Austin, TX