Seems like you want more for the same price. More outlets. Wireless built-in (reasonable). Support for all of the different light/pump setups. Breakout box. pH/ORP/temp/Salinity ports.
I can see how paying $500+ for a controller and then needing to add modules to get all the functionality that you want is expensive, but the market has already established that it is willing to pay the price. It's not about how much it costs for R&D and production, it's what the people are willing to pay for your product. Even if Apex (or anyone else) is able to produce exactly what you want and still turn a profit, they'd just price it at a premium for the added features. What you're asking for is for a company to produce a superior product and price it at a price that is lower than what the market is willing to pay. Essentially you want more for less.
Also, modularity is not necessarily a bad thing, especially in the aquarium industry. It sucks to have to buy all these add-on's to get the functionality you want, but there are just too many different proprietary connections to have it all in one base unit. Take lighting for example. The main players in LED are AI, Ecotech, and Kessil. All of which have their own wireless protocol (Kessil AP700 is wireless I believe, but the A360WE's use an analog signal via 3.5mm cable).
What happens when these need to be updated on the software side? You say it's a simple upgrade, but juggling all of the bug fixes and updates for just these three fixtures is very difficult and time consuming for a single company. On top of that, I'm assuming you'll be using a phone/tablet/browser, then you'll have to update all the separate devices in different software languages for all of the different software versions (iOS 7 vs iOS 8, Jelly bean vs Ice cream sandwich, Chrome vs Firefox vs Safari). It's not that easy.
What about the Chinese fixtures that MANY people use? Or the smaller, but quality companies like Nano Box? What if a new player comes into the LED game and gains popularity, say if Jebao released a light. If only there was a way to accommodate all this diversity and not have the consumer pay for all the connections/features they want or do not want.
Sorry to pile it on, but you do bring up some good points and this is how innovation starts. I just don't think you've thought it through all the way. A more reasonable approach for Neptune is to update (not overhaul) their current controller with built in wireless and maybe have some more ports built into the base unit. This is basically the Digital Aquatics Archon controller and (correct me if I'm wrong) it's not doing well.