You can negotiate with Stripe if you're at high enough volumes. It's likely that the "best" choice of payment processor is heavily dependent on the specific business in question. If you need agility and developer friendliness, Stripe is hard to beat. If you're trying to grind out every last percent of margin, you'll have to shop around and see what you can negotiate (and the offers you get will likely depend on the nature of your business, chargebacks/fraud, etc).
I have to admit I was thinking primarily of my company's use case, which is serving brick-and-mortar. This is a pretty different picture from card-not-present transactions, but if you're a low-risk business from the point of view of credit card processors, 2.9% is still at the high end. If you're brick-and-mortar, you can get rates as low as .25% sometimes.
Fattmerchant, Gravity Payments, and Worldpay are all great options for brick and mortar, and offer online payments too. Paypal is also cheaper than Stripe for US businesses.
As always, it depends, and it's complex. I probably was too confident in my above answer.
Stripe is an aggregator, which means they collect all payments and distribute to their clientele. This is why merchant processors like Square and Stripe can often get their customers up and running more quickly. Lower underwriting requirements = less regulation on the merchant. The level of risk is higher so they have to charge higher rates to cover their losses of fraud.
Gravity Payments is an Independent Sales Organization (ISO) which means they underwrite each merchant and "approve" each merchant account with their backend processor. This equals less fraud and more flexible pricing.
We do offer integrations and also have an online product that can process ecomm transactions for developer usage.