Marco della Cava

USA TODAY

SAN FRANCISCO — Call it Wal-Mart versus Apple. QR codes versus NFC. Checking accounts versus credit cards.

Whatever you call it, when two pharmacy chains recently disabled Apple Pay in their stores, it was clear the battle line was drawn in the coming mobile payments war.

On one side is a consortium of retailers including CVS and Wal-Mart that has agreed to next year implement a QR code-based app from Merchant Consumer Exchange (MCX) called CurrentC. On the other, near-field communications (NFC) options such as Apple Pay and Google Wallet.

Both warring forces are powerful. MCX's group represents roughly 50 retail partners — from Best Buy to Target — that process nearly $1 trillion in annual sales. And Apple Pay's exceedingly easy system — place your iPhone 6 near an NFC device and you're done — saw 1 million credit cards enrolled in the service's first 72 hours.

But, mobile payment experts say, a more powerful army may yet decide the payment system victor: consumers.

"This skirmish will go on for a while, but ultimately it seems shortsighted to tell customers that you can't use their competitor's alternative," says Matt Schulz, industry analyst with Creditcards.com. "The baseline really is the credit card. The process of using one is still very easy, so everything compares to that."

While acknowledging the power of the MCX group, Sterne Agee analyst Tom McCrohan believes almost all retailers will have to offer an NFC option "or risk losing customers. If McDonald's offers Apple Pay, do you think Burger King won't want to?"

When CVS and Rite Aid abruptly shut down Apple Pay, some customers angrily tweeted they would take their business elsewhere. The retailers had been forced to drop Apple Pay because of MCX's requirement that its group members not offer competing services.

In the immediate aftermath, MCX executives confirmed the exclusivity deal, but denied reports that members who wanted to opt out of CurrentC would be fined.

Drill down deeper into what's at stake and the first issue that surfaces is the matter of credit card fees.

Somewhat famously, former Wal-mart CEO Lee Scott was asked at a conference last year whether he felt confident CurrectC would succeed. Scott's response: "I don't know that it will, and I don't care. As long as Visa suffers."

Retailers like the MCX model because credit card companies cut into a retailer's profits to the tune of around 2%, often the very margin at which some low-cost stores operate.

CurrentC ties payments to a merchant-issued credit or debit card, or a checking account. Being privy to consumer shopping details in turn allows the retailer to mine consumer habits for its loyalty program. In a recent blog post, the company notes it "has plans to add additional forms of payment, including credit cards," but offers no timeline.

CurrentC app users will have to weigh the multi-step process of firing up an app and scanning a QR code against being tied into a proprietary rewards system.

"If you're a retailer and want to stay competitive, you have to think hard about what payment system to use," says Mallory Duncan, senior vice president of the National Retail Federation.

"The things they're considering are security, costs and flexibility, and any system will have to balance all three," says Duncan, who notes that ultimately credit card fees often mean a retailer must charge customers more. "There are complex issues at play, but ultimately the market will decide."

The NFC option, and specifically Apple Pay, offers consumers a painless payment experience while promising credit card information security since those details are stored not in the cloud but on users' phones.

"Ease of use is so incredibly important as a factor here," says McCrohan. "Past (mobile payment) failures were all due to inconvenience. If what you're offering isn't easier than swiping a card, customers may not bother."

The risk of losing a consumer over a clunky mobile payment option is a real issue, says Zach Goldstein, CEO of Thanx, a new customer retention app.

"Friction is a challenge with many loyalty programs, and if a customer forgets about you often there's little you can do to get them back," says Goldstein. "The math all retailers will be doing is, is it worth saving money on credit card fees at the risk of losing a customer who thinks your mobile payment is too cumbersome."

The notion of creating a system completely decoupled from credit cards isn't realistic, says Jason Oxman, CEO of the Electronic Transactions Association, which advocates for companies selling electronic payment products.

"The focus here should be on consumers, and in 2013, they spent $4.9 trillion using credit cards," says Oxman. "As we move into a mobile payment world, why wouldn't you as a retailer not allow your customers to use a system they want to use?"

The consensus is that, at least in the short term, the only point-of-sale solution consumers will roundly support is one that involves a range of mobile payment options.

"There's no way CurrentC can ignore NFC payments, so a collaboration is inevitable," says Patrick Moorhead of Moor Insights & Strategy. All checkout counters "will have to include a QR code readers, NFC and an old-fashioned credit card swiper."

Moorhead says that every consumer does his or her own personal calculus when it comes to the best way to pay, often weighing speed at checkout against the possibility of saving a few cents or dollars through a loyalty-based program. He also says that data safety is a growing concern that, for some shoppers, will trump saving money at checkout.

"Credit cards have worked for so long, and with good reason," says Moorhead, specifically spotlighting the fraud-detection services such companies offer. "Moving away from them is a losing battle."