For me, it seems like most of the things that some consider cons, I consider pros.
For example, a typical con listed goes like this. "For the price, all you're getting is a bunch of brackets. Other lifts, for the same price, give you more adjustable parts". To me, the pro in that statement is those brackets have a ton of engineering behind them to move stock parts to the specific angles that give your JK the ride that AEV is renown for. IMO, adjustable parts alone can't do that.
On the same note, another frequently mentioned con is "AEV lifts are non-adjustable". Somewhat true -- you can switch between 3.5" and 4.5" springs, but that's about it. There is nothing about the lift to adjust or "dial-in" after installation. To me, that's a pro. At the end of installing the lift, your axles are centered and your caster is restored. No messing around trying to find the precise lengths for adjustable trackbars/control arms to achieve those characteristics. To others, that's a con. They want to be able to tweak the characteristics of their ride. For me, it rides awesome immediately post lift, and I wouldn't want to tweak anything.
To address issues that are normally corrected by buying front control arms, AEV uses a control arm drop bracket. This bracket ends up slightly changing the angle of your stock lower control arms, and majorly changes the angle of the upper control arms. The pros are that it addresses a lot of drive issues, like flighty steering, reducing the front-end dive that happens if you nail your breaks, bumps feeling less jarring, less drive-shaft vertical travel, etc. Also, the bushings on the stock control arms are supposed to be better than aftermarket control arms, but I don't have any personal experience with that. The con is that it leaves your front control arms sitting a little below the frame level.
The Premium lifts also include the AEV jack base (which lets you use your stock jack in sand/mud, also lifts your stock jack up so it works with bigger tires) and the AEV ProCal (which reprograms your JK for bigger tire/gears/other features). IMO, both are useful tools and their value should be considered into the price. Even if you don't need them, you can easily resell them and pocket the cash.
I really really really like my AEV 3.5 Premium lift. I love how my JK handles on-road (especially how there's less body roll in corners than stock, even though it sits about 5" higher than stock now), and I've had no problems off-road with it. I'm actually not allowed to lead when my Jeep club goes on trail rides because I barely feel the bumps and ruts that really jar them, so I "go too fast". And granted, I'm Mid-Atlantic, so there's not a bunch of huge West Coast/AZ type of rocks out here, but my 4-door JK with the AEV lift has been able to crawl over everything that other JKs with similar height lifts have.