1). My stock sub was blown, so I had to either unhook it or replace it. OEM was way too high and no performance gain, this setup was cheaper and most definitely an improvement.
2). I've not got experience with too many different subs, but out of what I have had, I still think this is the best quality system I've personally had.
I'm really happy with it, overall I feel it was very worthwhile. I helped another member install a new head unit a week or so ago, and I was amazed at how much better his sounded with just a new head unit. I liked it so much that I've now got a new h/u on it's way, hope to have it installed next week. We'll see how much of a difference that makes, but if it does anything like I expect, it'll be awesome. I don't know that I'd do anything different in my situation. Once my head unit is done, I'll compare my setup to stock, it's been so long since I've heard the OEM system I can't recall exactly. Our setups are similar, only mine will have the aftermarket amp/sub. I'll post an update then.
I feel for the money and specs, the equipment I chose is the best fit. The w3 is a better sub, but requires more modification to fit (and a custom spacer to be made). For what it took to install mine, I'm fully satisfied.
The amp only powers the sub, the stock JBL amp still powers all other speakers (just not the sub anymore).