Both models are based on a spread, which has to be as stationary / mean reverting as possible.
$ y_t = \beta_0 + \beta_1 x_t + \epsilon_t $
In pairs trading, $y_t$ and $x_t$ are log prices, and (e.g.) the Johansen cointegration test is used to identify candidates for a pairs trade. For entry and exit points an error correction model is used. In the Avellaneda & Lee (AL) paper the $y_t$ and $x_t$ are indeed the returns. Mean reversion is modeled as an Ornstein-Uhlenbeck process on the cumulated residuals
$ X_k = \sum_{t=1}^k \epsilon_t,\ \ k = 1,2,...,T$
which are stationary (mean zero) by construction. Since the residuals are cumulated or 'integrated' they are stable and may display mean reversion, much like in traditional pairs trading.
I see two important differences: the AL method is (as the title says) a statistical arbitrage approach where $x_t$ are risk factors or baskets of securities, such as the PCA and ETF examples in the paper: it is not limited to pairs. Also, in AL there is no explicit test of the cointegration strength, as the mean reversion is built into the model.
Pairs trading is the basic buy cheap sell expensive strategy. That kind of strategy, just did not work the next year. In fact, the opposite was true. Buy expensive stock... and hold it.
– Wilmer E. Henao Dec 14 '13 at 03:27