I think it would come down to price. One of the HT mags did a "Sub Shootout" a couple of months ago and the S120PII was the top rated "low price" sub (Only in our hobby would a $799 MSRP sub be low price!!!). I have one in my bedroom HT and I think it is a nice little sub. You can find it online for less than $400...
I'll second that. The S120PII is a great sub for the money, especially at the prices it can be had for. I've seen it as low as $299 "buy it now" and regularly $374 "buy it now." For a 400W, 12" sub, that's a great price. Also, it's very flexible in the ways that you can set it up and connect it to your system.
Occasionally, JBL direct has a refurbished unit on auction somewhere (like eBay) that typically starts at $1.00; sometimes these go for around $200 or so, and they come with a full factory warranty.
The Alpha's advantage will be it's RABOS (parametric EQ) feature. It's a great tool for improving (flattening) bass response in the room. I'm assuming the Alpha is more expensive though, so you must decide if the extra money is worth it. Depending upon your room shape and where you intend to place the sub, having the ability to flatten your rooms major "bass peak" can greatly improve sound quality. Knowing I could've had a Hsu or SVS sub that plays louder and lower for the same money, I would still take my Interlude IL120s (the Alpha subs predecessor) just because of it's RABOS feature.
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