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Easy.. One is a positive displacement blower and one a centrifugal. Whipple will start out extremely strong and lose steam at upper rpm. Procharger is a more linear and predictable power curve and easier on parts.
Depending on the size of the Procharger you can make significantly more power up top. Also with the Procharger cones the opportunity to add port injection aka an extra 8 injectors. You can't do that with a positive displacement blower. So you'll have more headroom in fueling with the Procharger.
Personally I went with the Whipple because it suits my driving style and likely will be easier for me to install. Plus it was much cheaper.
There are a couple examples out there of the Whipple 2.9L over 900rwhp so big power is possible just not at the level of a big Procharger.
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