An alternative to ADK is the Android USB Host driver support. It's like libusb: for phones with the right USB controller, you can write little drivers in Java/userspace.
Here's an Android library you can use to talk to almost any Arduino, great for these type of "make my microcontroller smarter" applications: https://github.com/mik3y/usb-serial-for-android (full disclosure: I'm the author)
I would agree. I created the Handbag for Android project (http://handbagdevices.com/) which was initially based on the ADK so I've spent a lot of time with it. In the ADK 2.0 release Google itself even moved away from having the physical USB link in favour of using Bluetooth.
When 2.0 was released I started converting Handbag to have the option of Bluetooth/WiFi/USB but the ADK stuff was so unreliable (and the debugging was ridiculous due to different issues on each Android version available at the time (2.x/3.x/4.x)) that it seemed like a waste of time to continue.
The goal of Handbag was to enable an Arduino sketch to create an Android UI and have bi-directional communication between the two devices. It could be interesting to adapt that aspect to run with the linked project.
Then the only time I heard of anyone owning the ADK was my friend who worked at Google. It seems they kindof gave them out as party favors. I thought it was a great idea & wished it would take off but unfortunately had to move away from Arduino anyway to focus on web engineering career and to this day(!) I don't own a smartphone.
in the longer term, there are already microcontrollers that contains Bluetooth who run arduino, so I believe this project will become only software.
If only there was some way to take advantage of all those hardware capabilities on the phone without the hassle of hooking up an Arduino. If only there was some sort of way to write 'programs' that take advantage of that hardware. But 'programs' sounds boring, we'll call them 'applications'. Wait, no...that has too many letters. I know! We'll call them 'apps'! You're gonna love 'em, they're the next big thing.
Oh wait, a smartphone's hardware is closed, you get what you get (in terms of sensors and control) and thats it.
Hmm. It would be nice if we could extend the smartphone's hardware capabilities...
on a more serious note, I'd love to see more widespread generic HW and SW agnostic GPIO/DAQ standard. HW agnostic meaning that you could make your own boards with whatever MCU you prefer, and interface it with whatever. SW agnostic so that it would work with Windows, Linux, Android, OSX, iOS etc painlessly.
Hell, most of the devices have support for inter-platform RS232. You should be able to communicate between an Arduino and an MSP430 via RS232 (you might need some resistors in the middle, because I think one runs 1.7v hotter than the other).
The hardware situation is fragmented because I think people want the one-device-one-shield model. I don't think they want to deal with daughter boards dangling from adapter cables. The majority of users for these systems are either hardware novices or hardware-and-software novices. Most of the electrical engineers I know steer a wide birth away from them. And once they get invested in a platform like Arduino, jumping over to something like TI MSP430 is an effort that is at least as significant of an effort from where they started, while providing only a limited, non-obvious benefit (in that MSP430s are cheeeeaaaap).
Interestingly the linked project appears to be based on Firmata which has at least some of the agnosticism you seek.