Hey bud, I went through what you are going through now. You can check my thread here:
Basically, I have different needs than you. I like the frame-less windows for looks but I have dogs so I need to be able to slide them open and they love the screens and air. If I didn't get the normal slide windows, I would have gotten the fold down windoors for the side as well (strictly because I load up my bed a lot and it would be nice to be able to open the window and grab things near the back). For looks, the frameless hands down.
I just got my topper and drove almost 4k miles across the US. I have the Yakima rack system with a Thule surfboard lockable rack. Didn't leak at all despite driving through hurricane downpours are the time and I had tons of valuable stuff in the back (paintings, art, etc).
The ARE Topper is killer. I have no regrets on my choice at all. I did my research and looked at the toppers at the different dealers in person (SnugTop was not on the list because of the amount of time it took from order to delivery). Not all toppers are built the same, not all paint is the same and not all the fit and finish is the same. My second choice was the LEER brand but they had 2 draw backs as far as I was concerned. 1 was the amount of people who made posts about the paint but then as I went out and looked at used toppers, sure enough, the LEER's had way more paint problems than the ARE (fading, cracking/crazing, etc). Then, the second was the LEER dealer in my area was a total douche. I wouldn't give him the gum off the bottom of my shoe, let alone a big money purchase like that.
The other things I like about the features are the fold down rear windoor. I used this several times during my trip and 'yes' it lines up with the Tacoma back window (pretty damn close). Other toppers did NOT line up well. I also really like the slam latch instead of the twist knob and if I had the extra money I would have gotten the remote entry too. I had the twist knob on my Gen 1 and even though I liked the old topper, the new design is way better. The carpet is awesome and I also got one of those hanger doodads which has been used for a lot more than just hanging clothes from it. It's also great because you can't open/steal the gate with the back window closed and locked (well not easily, one could break it but then again they could just break the windows so...).
In retrospect I remember thinking I might have regrets with the purchase but I can honestly say I don't have one. Good luck with your purchase!