Okay, after spending more time being indecisive about this than any other topic in recent history, I've decided that I'm going with the BakFlip MX4. Here's why... what works for you will obviously be a bit different.
RetraxPro XR was top of my list for a while. But, after seeing that the cover takes up about a foot of bed space, I was discouraged. My AT4 only has a 5'8" bed. I need all the space I can get. Also, if i need my full bed, it's not that easy to remove (in comparison to other models). Also, price is pretty high, though I know quality is great, you get a limited lifetime warranty, and it would be great to have those extra rails. However, I don't have any Kayaks , or anything else that would require me to stack cargo with a Thule rack that I couldn't put in my trailer... so, I moved on.
Lomax Trifold. I'm not sure there's another cover that looks as good and is as low profile as this one. It's great looking. I love that you can remove the entire thing pretty easily if you need your whole bed. However, that also means that the cover can literally be easily stolen if fully open. Not much is keeping it secured to the rails. Also, I did not like that it doesn't lock after the first fold. Finally, it does not fold up vertically to allow 100% bed access. And, when folded all the way up, and strapped in, it takes up as much, if not more bed space than the Retrax. The only way you get to use your whole bed is if you take the whole thing out.
Undercover Ultraflex. Also looks great and is VERY similar to the BakFlip. Love that it has a better warranty than the BakFlip (5 yrs), has a carpeted undercarriage, and comes with some freebies (cargo bag and LED lights). While not as easy to remove in comparison to the Lomax, it is still relatively easy to remove, should you need the whole bed space. However, you can also fold it up VERTICALLY to get near complete bed utilization. The one thing that turned me off was that it DOESN'T lean on your window and sits vertically. I've read reviews that when in the vertical position, it is still somewhat flimsy and your top brake light may be blocked entirely (as is the window).
Why I'm going with the BakFlip... All the positives of the Undercover -- full bed usage, locking segments, can be removed rather easily. However, it leans against your window when fully open, allowing slight visibility out the window and full visibility of your top brake light/cargo light for following vehicles. Some downsides: I've read that Bakflip quality has waned in the last few years and the warranty is only 3 yrs. But, it's the best selling hard top trifold on the planet for a reason and the company has improved the model in the past few years (allowing for closure of the cover with and without tailgate open.
Hope my train of thought helps folks decide. Do what will work best for you. I'll note that I too haven't purchased a cover. This is all based on my review of other reviews and what I think will work best for me.