"It's a curse and blessing to have a really high return on invested capital," Trainer said. He noted that with such a high metric—which at one point hit 330 percent, dropping to 227 percent in 2012—any company would invite a large amount of competition.
The current stock price implies a 124 percent ROIC, Trainer estimates. "I think that that's an unsustainably high level of return on capital for any business, much less one that's competing in a cut-throat business like consumer electronics. I don't really think they can justify the valuation they have," he said.
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An expectation that Apple will revolutionize another industry like they did with the iPhone and iPad is a "home run" bet, Trainer said, noting that its competition now has comparable products. "When they started, the iPhone there was nothing else like that. Now you've got a lot of products that are very, very similar and some people will argue that the Samsung Galaxy is a better phone," he said.
Trainer added: "I'd rather not bet on someone being able to revolutionize some new market again. I think it's important not to underestimate the impact of Steve Jobs. He did amazing things we may never see again. Steve Jobs was a singular personality that took Apple to new heights."
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If Apple's ROIC was the same as Microsoft—at 75 percent—the stock would be valued at $295. In contrast Google's ROIC stands at 34 percent, which would place Apple at $191. He's pegged his expectation for Apple's metric in the middle, at 50 percent, in his valuation. Trainer's analysis takes into account NOPAT (net operating profit after taxes), cash per share, minus debt, option liabilities, deferred tax liabilities that brings him to a $240 equity value.
Trainer used a discounted cash flows method that is outlined in a blog post he wrote on Tuesday, which can be accessed here.
—By CNBC's Paul Toscano.
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Neither Trainer or his firm hold a position in Apple stock.