In 2012, investors’ long-harbored suspicion that the stock market was a rigged game became something of a majority opinion.

This year, exasperation over the predominantly electronic mechanics of trading stocks, in which hyper-fast computer algorithms maneuver against one another for fractions of pennies collected over microseconds, boiled over. The level of disgust has gotten broad enough, in fact, that authorities might be prepared to rethink some of the basic rules and processes driving the system.

The opaque and complex structure for trading stocks electronically across dozens of exchanges and alternative networks has long been justified by industry leaders and regulators as the messy but logical result of investor-friendly reforms. Technology has enabled mind-melting speed, unfathomable communications capacity and brutal competition for order flow – all of which have made trading cheaper and faster than ever.

Yet by squeezing out traditional market makers who once collected low-risk, protected profits by mediating among buyers and sellers, rules and technology have tilted the power toward “high-frequency traders.” And in 2012, the fragility produced by so much layered complexity became too obvious, and produced too many market-jarring failures, to be considered merely the price of progress.

A List of Failures

In March of 2012, BATS Trading, an upstart exchange that sees a large percentage of its volume from HFT firms, botched its own initial public offering. First unable to process the initial trades, BATS ultimately canceled the IPO.

In May, the Facebook (FB) initial public offering was mishandled by Nasdaq, whose systems couldn’t keep up with the flood of electric orders. Many small investors just mustering the will to wade back into the market to own a piece of FB were turned off by the fiasco.

Only months later, Knight Capital Group (KCG), a premier electronic stockbroker and market maker, nearly went under when a trading-software upgrade went rogue and spewed orders without human intention or limit. Knight is now being acquired by HFT powerhouse Getco.

A process that began in 2000, when regulators and exchanges moved to quote stocks in pennies -- making it easier for automated scalpers to “improve” a quote by one cent to legally front-run real orders while reducing the amount of stock behind each bid or offer -- has now agglomerated to a point that almost no one is satisfied. A recent publication of the staid New York Society of Security Analysts declared that “public confidence in the integrity of equity trading markets appears to be at a once-in-a-generation low.” This is a trend measured in the nearly $300 billion retail investors have yanked from traditional equity mutual funds since 2009.

Do Robots Really Run the Market?

But do the hyper-fast, disembodied trading robots really run the market for their own profit?

There is some irony in the fact that the public is so embittered about what they believe to be a market rigged against them, when, for most, stock trading has never been easier or less costly. For a flat $8 commission, a stay-at-home investor can instantly execute a trade in almost any stock with little noticeable friction. If, at times, an opportunistic algorithm steps ahead of that order by, say, bidding a penny more and driving the price up a couple of cents, that charge is vastly less than the 25-cent spread Nasdaq market makers used to take on almost every trade. If anything, the small investor is better served by the current trading arrangements than are large institutional investors, whose need to execute large, sensitive orders is compromised by the software spies’ efforts to step in front of their trading flows.

Indeed, even the dominance of high-frequency trading, once said to participate in a sizable majority of stock orders, has passed its peak, thanks to competition and lower market volatility reducing their opportunities.

Still, somehow the opacity and bloodlessness of the automated quasi market-makers rankles more, especially when investors are less confident of unending stock market appreciation than they were in the late 1990s and early 2000s.

Perception Becomes Reality

The measure of disaffection with today’s market structure by both professionals and individuals means that, even if the financial impact to the typical trader isn’t onerous, the sour perception in itself diminishes market quality and vitality.

And sentiment isn’t helped by the ongoing round-up of alleged insider-trading conspirators among employees of major investment firms, which has made headlines that prove the authorities are paying attention while also hinting to the little guy that investing profits are often ill-gotten.

The good news in all the frustration with our tangled trading system is a renewed focus on rationalizing it. At a Senate Banking Committee hearing on electronic trading in late December, a rough consensus among exchange officials showed a desire for Congress to lay out clearer order-handling rules. The recently announced merger of electronic derivatives exchange ICE with NYSE Euronext could provide further impetus for a fresh look at the trading landscape.

Several years ago, Jim Maguire -- a NYSE floor veteran and longtime specialist for Warren Buffett’s Berkshire Hathaway Inc. (BRKA, BRKB) shares -- began promoting a small but potentially helpful reform: quoting stocks in minimum increments of nickels rather than pennies. The idea was to create greater incentive for middlemen to provide a deep and fair market for public orders. Dubbed “Mr. Nickel” by Barron’s, Maguire was viewed as a charming little anachronism.  Yet on Feb. 5, the SEC is holding a panel discussion to discuss “the impact of tick sizes on securities markets.” There is also now a more open discussion over charging high-speed traders for the massive system capacity they use.

The now deeply ingrained sense that stock trading is a game rigged by privileged sharpies with their omnipotent machines will not dissipate soon or easily. But as we enter 2013, it appears at last that those able to take action to foster greater faith in the integrity of the markets are at least focused on the issue.