There are a lot of reasons why pasta sauce from a bottle or can is inferior to sauce made from fresh ingredients. Aside from the usual processed vs. fresh complaints about metallic flavors, preservatives and high sodium levels, the fact is that a lot of things that make fresh sauce good just aren't possible or practical in mass production. Certain chemical reactions either can't happen reliably in a giant vat or won't survive long after the lid gets sealed. There are a few key players in the surprisingly nuanced science of red sauce. Namely, they are tomatoes, wine, herbs and time.
Let's start with what seems like the most straightforward but is actually the most variable ingredient, tomatoes. Now, a lot of pasta sauce recipes calls for some crazy combination of fresh tomatoes, tomato paste, crushed tomatoes, diced tomatoes and just about any other form of the fruit, but that's just a leftover issue from bygone days of supermarket fever. Fresh is all you need and fresh is all you really want, for a lot of reasons. Chiefly, fresh tomatoes don't have any added salt or sugar, which makes it possible for you to tightly control the seasoning in your sauce. Too much salt or sugar will overpower your sauce no matter what else you do to it. Honestly, tomatoes have enough moisture and structure that pastes and other forms simply aren't necessary, not when you consider the importance of...
...Time. The best pasta sauces simmer on the stove all day and with good reason. Getting that thick consistency everyone loves is simply a matter of letting the water slowly boil out of the mixture. Let this happen too quickly (re: on too high a heat setting) and you'll burn the solids in your sauce. A very low, steady heat will reduce your sauce in a way that both thickens it smoothly and brings out some of the natural sweetness of the tomatoes.
But we're not done with tomatoes just yet. Not when wine is involved. In addition to bringing a lot of flavor to the sauce on its own, wine has the added advantage of containing that chemical powerhouse, ethanol. Yes, drinking alcohol has many culinary applications, including the ability to interact with the molecular structure of fruit to unlock delicious flavors that aren't otherwise possible. This is why vodka is such a common ingredient in gourmet tomato sauces. Wine is softer in flavor, so letting it serve as a part of your sauce's base is a great way to get the most out of your fruit.
Herbs are the biggest flavor components in pasta sauce, most notably garlic. The rule is, if you think you're using enough garlic, you're not. The stuff is inexpensive, so don't be shy about throwing a large number of cloves into your sauce. It's remarkably difficult to make a sauce taste "too garlicky", especially among all those other flavors. But other heavy hitters like basil, rosemary and oregano are just as important. As with the tomatoes, use fresh herbs. They have more taste and they add a refreshing bouquet to the sauce that dried stuff just can't replicate.
Of course, fresh ingredients are impossible in mass produced sauces. Even if fresh things go into the sauce at production, they aren't fresh anymore when you finally get your hands on the sauce. The use of alcohol is financially problematic at best and waiting for a vast quantity of sauce to simmer all day, taste testing the whole time, is simply not feasible. If you want the finest, most flavorful and healthiest pasta sauce, you have to build it with care from fresh ingredients. It's well worth the time and effort.