Why is the dough in cheap pizza places so bad?

Well, the most obvious difference is that the two "better" restaurants you mention serve brick-oven style pizza, which is probably quite different from the cooking method in a "cheap sub-style pizza place." Brick oven pizzas are generally cooked at a much higher temperature for a much shorter time, and the surface they are cooked on causes significant changes to the crust. You'll get much greater oven spring, a crisper outer crust layer, a dryer bottom crust, and a softer interior due to the oven spring and short bake.

All those things already will make a huge difference in crust characteristics. But the dough you're describing (rubbery, spongy, few bubbles) also sounds a bit underdeveloped. Higher-quality pizza shops will often allow a longer time for fermentation (which also increases flavor, as well as producing better texture); the stuff you describe may be "rushed" somewhat.

Although you say "thin crust," I'm assuming you're not talking about the thinness of, say, NY Style, but rather an intermediate crust depth (not as much as "Sicilian" but not as thin as brick oven, Neapolitan, or NY Styles). At least that's the kind of crust I associate with the kind of "sub-shop" pizza you're describing.

If that's correct, there could be other problems too. Places like that may not have confident workers stretching the dough, and they overcompensate to avoid tears or holes -- this means they often don't stretch the dough as thinly, may roll out the dough and deflate it a bit, may use a lower hydration dough (which is easier to handle), and may use a higher-gluten flour. Lower hydration doughs can often produce a denser and less tender product. Moreover, high-gluten flour will toughen significantly as the pizza begins to cool, and a thicker crust improperly baked may also have a "gum line" right below the ingredients where the dough isn't cooked as thoroughly. The moisture from that gum line can also migrate down to the crust during cooling and toughen the crust. Pizza packaging can also make a difference here: those rippled sheets some places put pizza on help to take moisture away and avoid some of the toughening in heavier crusts; without them, a dense dough can also toughen.

To sum up, here are a few things that may be contributing to the "rubbery" experience compared to your preferred brick-oven style:

• higher gluten flour (when used inappropriately)
• low dough hydration
• inadequate fermentation time
• inadequate rest after shaping
• heavy rolling out of dough, rather than stretching
• lower oven temp
• less ideal baking surface
• longer bake time
• thick or medium crust not baked through
• bad packaging

There are other possible causes, but I imagine these are part of the issues you've experienced.

As for the hypothesis of frozen or pre-made dough, that could be an issue, but there's no reason pre-made frozen dough necessarily will produce bad crust. (There will generally be some quality loss, but it's mostly flavor.) It's perfectly possible to make a tender, flavorful, non-rubbery crust with frozen dough (assuming the proper recipe). Frozen dough might contribute to the problem if defrosting and proofing time is inadequate; while convenient, frozen dough needs plenty of time to thaw and get ready before baking.

That said, a final issue in some pizza places may be dough schedule. A lot of small-scale pizza shops don't make new batches of dough every day, and if they aren't careful about storage and prep, the dough that's "too young" or "too old" may have undesirable characteristics, including bad texture. (As mentioned above, your description sounds like "too young" dough, if anything.)

I did some more research on this question and found that the reason cheap pizza places tend to have similar, low-quality crust is because they use something called "parbaked" dough. This is dough that has been made ahead of time in a factory and partially baked. Various suppliers sell this to hole in the wall pizza places. For example, in my area, "The Pizza Company" is such a supplier. The advantage of this is that the pizza parlor cooks do not have to make the dough, and they can store it for several weeks.

Parbaked dough is usually leavened with artificial leavening agents, such as baking powder. This is why it has a bready texture. Using yeast is much more difficult and requires human judgement. By using artificial leavening agents it is easier to control the process. The rubbery-ness comes from freezing or refrigerating the dough. Whenever dough is not immediately cooked into a crust fresh and it is stored, it will deteriorate and become rubbery. One way to disguise this is use little or no leavening agent and make a very thick crust. This is the theory behind "deep dish" pizza. By making a thick, unleavened crust with added fats, it can be refrigerated or frozen and the rubbery texture is not as noticeable because it is so thick and stiff. It is sort of like a poor man's pastry. Deep dish pizza is profitable because they use cheap greases and fats in the crust, allowing them to use a vegetable heavy topping with little or no cheese. Since synthetic shortening is cheap and cheese is expensive, the "deep dish" style is much cheaper to make.

Real Neapolitan crust, the original form of pizza, has only four ingredients: flour, water, salt and yeast. Freshly made dough must be carefully monitored, so that it rises the proper amount, which takes several hours. The cook pokes the dough with his finger to know when it is ready. The dough must also be kneaded by hand--another non-starter for cheap places that do not have time to do such things. The dough must be cooked the same day, made fresh in the morning and then used by the end of the day. The dough cannot be allowed to dry out, or it will form a skin. Dough which is not used by the end of the day is worthless and must be thrown out.* The delicate, time-sensitive and laborious nature of this process is why it is not practical for sub shops to use fresh dough.

*The problem of excess dough is solved in a creative way by Bertucci's, a chain in the Boston area. What they do is turn extra dough into rolls. So, when they are running an oversupply of dough, they give more "free rolls" to their diners, but when dough is tighter for the day, they give out fewer rolls. By using rolls to buffer their dough supply they can greatly reduce the amount they have to discard.