I love Giordano's; in fact, it's my favorite of all the Chicago deep-dish pizzas. What I like best about it is both the center filled part of the pizza, for its blended taste of crust/cheese/sauce/toppings, as well as the super-delicious outer crust, which should be crisp and tasty. From the description above, it sounds like the lunch mini-pizzas (which I've never had) don't measure up to the made-to-order full-size versions.
I also don't like the pizza at Pequod's or Burt's; I just don't enjoy their burnt crust. I also find that the rest of the pizza is just meh, and doesn't have the delicious taste of Malnati's/Uno's/Gino's/Pizano's for single-crust "pan" pizza (or Giordano's/Edwardo's/Bacino's for double-crust "stuffed" pizza). However, I can understand why people like them for their funky off-beat decor and, in the case of Burt's, for Burt and Sharon's friendly hospitality.
Also, I don't consider mail-order or store-bought frozen pizza to be adequate representations of the real thing. Home ovens don't have the high heat of the ovens found in pizza parlors, and there may be other reasons, but in any case, my experience is that they're not as good as freshly-made pizza at the restaurant (for just about any brand name).
Most of the big pizza chains have multiple locations in the downtown area; look on their websites for specific locations. In the Loop itself, you'll find Giordano's, Pizano's, Bacino's, and in surrounding neighborhoods (South Loop, River North, etc), you'll find all the rest of the big names. All of which IMHO serve excellent pizza.
De gustibus non est disputandum.