DISCLOSURE: I'm a neptune insider. bias implied
I have the Apex 2016 on my main tank and an Apex Jr on my smaller one. I have a few friends who have the GHL Proflux 3 and one with a 4, and I just really enjoy fusion a lot more than I enjoy the GHL interface I've seen when talking with them. Over the course of the past year, 2 of them left the Proflux 3 for an Apex and the other proflux 3 went to a 4 after getting his wet.
If you go searching, you'll find people have bad experiences with any controller, but I've had a total of 3 issues with Neptune Systems products in the almost two years I've had mine. I did get one of the brains with the bad memory, it was fixed in a reasonable amount of time and right the first time. I did a bad thing with programming and had to get some assistance to restore the code, it was fixed right the first time on a Sunday. I got a WAV with a bad mount, that was fixed right the first time. Each time I did opt to place a deposit on a credit card for the advance replacement (that's for issue 1 and 3, issue 2 was resolved with a web ticket and phone call). I'm accustomed to doing this with other devices (keyboards, midi stuff) I have so it doesn't bother me. My friends have all had similar experiences with their GHL devices.
Personally, I think both are fine devices, and one of them will speak to you more than the others. Fusion and its programming get me every time. I like the way the programming lets me see both a graphical and code view of things for stuff like dossing, wave makers, variable speed controllers, lighting, etc. I really enjoy the DEFER and WHEN statements available in Fusion. I'm on the beta of the Fusion software and the IOS app and I really like the way they have listened to the insiders and added features/options we wanted. I also did the ATK preview, and they added the siphon break to the kit after many of us testers needing it. I've seen them first hand react to our suggestion and improve things. I like the pace at which they are moving as well. New devices and features of existing ones are arriving several times a year. That makes me feel like they are pushing the boundaries a bit, and I think their new module the Trident is proof of that. There are many Alk monitors starting to pop up, but not a three in one, and not connected to other controllers yet. They pushed the boundaries beyond the capabilities of their old controllers with that device much to peoples anguish, but I'm glad they are moving forward. I don't have to replace my Apex Jr. It'll do the same job it does today just fine, but I will because I want that Trident.
Also, whichever way you go. Always plan to have a way to keep your tank running manually. Electronics fail and they wait until you get comfortable for it to happen. I've had good experiences with my devices and others have not, same for my friends with GHL. Ultimately we were all okay because we had backup means to keep life happy while our controllers were being fixed. Plan for that, or it will arrange for you to learn the hard way.
Cheers,
Jason