Love the feedback from you guys, seeing as I have zero experience in a packraft...
Spray deck: At this point I'm pretty sure I don't want a spray deck. Since I'm just getting into it, I think I'll feel more comfortable not being "confined" in the boat. I know that in a worse case scenario, the spray skirts are easy to get out of, but just the simple idea of it all in the back of my head can be unsettling. I have 3 or 4 local rivers that I plan on rafting this summer, and they're all pretty mellow(I've floated them in $15 pool toy rafts in the past). With that, I really can only foresee myself using the raft during the summer or early fall, and plan on getting wet, which will be a welcome reprieve from the heat. And finally on this topic, I figure that I could make my own spray deck if it turns out that I like the NRS raft enough to not justify buying the alpacka. I've seen several people mod their Alpackas, and I'm pretty comfortable with MYOG stuff, so I'm kind of looking at it as another project if it gets to that point. Truly, the way I'm looking at it is, if I use it several times this summer, and find that I want to get further into it, then I can fork out the additional cash and get an Alpacka. At this point, spending $1,000(raft, paddle, etc) to get setup to do a sport that I've never done can be daunting, so minimizing that startup cost was a lot of it.
Flyweight: I did look into the Flytewater, their rugged version of the Flytepacker. It was on my list, but it appears to be much smaller than the NRS(over a foot shorter). This matters mainly for cargo room. I plan on being able to strap a bike to the front of the raft, so the large size of the NRS is welcomed by me. The weight listed for the Flytewater is one pound lighter than the NRS, while the NRS comes with a full inflatable floor, and seat, so aside from those, I think they're almost the same weight wise. And something about the Flytewater just doesn't look as sturdy, nor as "refined" with the lack of upturned bow. The tie out points look really weak, and that's compared to the Alpacka and NRS ones that people already complain about. I plan on adding some addition tie out points on the raft down the road. And again, the NRS wins with purchasing it through REI... Their warranty is simple and worth some peace of mind.
I look forward to getting my hands on it, and giving it some real use. There isn't a ton of information out there on the NRS rafts, so I'm hoping to learn a few things and be able to pass those on to others in a similar position as myself. Thank you guys again for bringing up very valid points!