I had mentioned frameless glass and it does look nice. My Super Sport has rear, wing opening windows.

However, if I still had dogs I would consider sliders on the side windows with removable screens.
This means Alu framed windows.

Snug makes a couple of models that look like the Super Sport model that I have, only with the side sliders.

Xtra Vision
http://www.snugtop.com/products/xtra-vision.php
The Rebel and Cab-Hi models feature side sliders at lower price points.

The optional Sportsman's package gets you a reinforced load bearing roof (Yakima Rack system available).
It's 1" thick so you can run screws up into it for rod racks, etc without punching through.
I told them to "ship loose" the included rod rack and clothes hanger.
Put them in yourself, where you want them.

There is $100 off coupon from corporate on line. I negotiated my price and then hit them with the coupon just to make sure that there was no price-padding to absorb the coupon.

Good luck, take your time and get what you want.