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To start off the conversation i feel that Java EE in earlier times had its set of flaws. In addition to that however, coding applications using proprietary APIs seems like a sure shot way to increase your development efforts down the line should you choose to scale up and move to a different vendor. You are correct in saying that WebLogic is much more forgiving when it comes to backwards compatibility; but i personally would always recommending sticking with the standard APIs than committing to the proprietary ones in case of any AppServer.
The advantage of Java over PHP would obviously be the much higher performance and scalability that it can achieve out of the box. For a quick set of comparisons take a look at the following link.