Older parts are being replaced by newer parts all the time. Not recommended for new designs is just Microchips way of letting the designer know certain parts are being phased out. If you're designing a new product you'll want to steer clear of parts being phased out.
If you're just working on one-off hobby projects, use anything you can get your hands on, but just remember the parts you use now may not be available down the road a ways.
Rohs compliance is a big factor, but Microchip was doing this long before Rohs was even an issue. Direct replacements that are just better, and different manufacturing techniques that make direct replacements less expensive to manufacture are also reasons for phasing out older parts.
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